Question: vsn preprocess with oligo package
0
gravatar for José LÓPEZ
6.9 years ago by
José LÓPEZ110
José LÓPEZ110 wrote:
Dear Benilton, I am using oligo for Mouse Gene 1.0ST arrays. In addition to RMA, I would also like to pre-process with vsn. I have seen previous threads related to this question in the past, (https://stat.ethz.ch/pipermail/bioconductor/2010-January/031100.html, https://stat.ethz.ch/pipermail/bioconductor/2010-June/033936.html), but unfortunately, I am not bioinformatician and, although I read oligo and vsn manuals, it is not easy to me to follow up to summarize the vsn object. May you (or someone else) please, give me some additional clue to sumarize the vsn object using the oligo package. Thank you very much in advance for your time and your kind help, Jose LOPEZ ************************** > list.files() [1] "ABRNA1.CEL" "ABRNA2.CEL" "ABRNA3.CEL" [4] "ABRNA4.CEL" "ABRNA5.CEL" "ABRNA6.CEL" [7] "Limma_FilterBefore_H2BGFP_jla_vsn.R" > library(limma) > library(oligo) Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following object(s) are masked from ‘package:stats’: xtabs The following object(s) are masked from ‘package:base’: anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique Loading required package: oligoClasses Loading package bit 1.1-9 package:bit (c) 2008-2012 Jens Oehlschlaegel (GPL-2) creators: bit bitwhich coercion: as.logical as.integer as.bit as.bitwhich which operator: ! & | xor != == querying: print length any all min max range sum summary bit access: length<- [ [<- [[ [[<- for more help type ?bit Loading package ff2.2-10 - getOption("fftempdir")=="/var/folders/U+/U+SFMmqcEbKkSysJQ3OYbk+++TQ /-Tmp-//RtmpKgQzWD" - getOption("ffextension")=="ff" - getOption("ffdrop")==TRUE - getOption("fffinonexit")==TRUE - getOption("ffpagesize")==65536 - getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes - getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system - getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system Welcome to oligoClasses version 1.20.0 Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. ====================================================================== ================================================== Welcome to oligo version 1.22.0 ====================================================================== ================================================== Attaching package: ‘oligo’ The following object(s) are masked from ‘package:limma’: backgroundCorrect > Data=read.celfiles(list.celfiles()) Loading required package: pd.mogene.1.0.st.v1 Loading required package: RSQLite Loading required package: DBI Platform design info loaded. Reading in : ABRNA1.CEL Reading in : ABRNA2.CEL Reading in : ABRNA3.CEL Reading in : ABRNA4.CEL Reading in : ABRNA5.CEL Reading in : ABRNA6.CEL > pms=pm(Data) > class(pms) [1] "matrix" > head(pms) ABRNA1.CEL ABRNA2.CEL ABRNA3.CEL ABRNA4.CEL ABRNA5.CEL ABRNA6.CEL 2106 46 43 36 36 37 33 2107 38 32 33 36 43 34 2108 31 31 35 34 37 35 2109 54 46 45 40 58 35 2110 58 55 40 39 94 40 2111 53 39 34 36 43 43 > pmsVSN=vsn::vsnMatrix(pms) vsn2: 899636 x 6 matrix (1 stratum). Please use 'meanSdPlot' to verify the fit. > class(pmsVSN) [1] "vsn" attr(,"package") [1] "vsn" > pmsVSN vsn object for n=899636 features and d=6 samples. sigsq=0.026 hx: 899636 x 6 matrix. > eset=rma(pmsVSN, background=FALSE,normalize=FALSE) Error in function (classes, fdef, mtable) : unable to find an inherited method for function ‘rma’ for signature ‘"vsn"’ > library(vsn) > meanSdPlot(pmsVSN) KernSmooth 2.23 loaded Copyright M. P. Wand 1997-2009 > sessionInfo() R version 2.15.2 (2012-10-26) Platform: i386-apple-darwin9.8.0/i386 (32-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] vsn_3.26.0 pd.mogene.1.0.st.v1_3.8.0 RSQLite_0.11.2 DBI_0.2-5 [5] oligo_1.22.0 Biobase_2.18.0 oligoClasses_1.20.0 BiocGenerics_0.4.0 [9] limma_3.14.3 loaded via a namespace (and not attached): [1] affxparser_1.30.0 affy_1.36.0 affyio_1.26.0 BiocInstaller_1.8.3 Biostrings_2.26.2 [6] bit_1.1-9 codetools_0.2-8 ff_2.2-10 foreach_1.4.0 GenomicRanges_1.10.5 [11] grid_2.15.2 IRanges_1.16.4 iterators_1.0.6 KernSmooth_2.23-8 lattice_0.20-10 [16] parallel_2.15.2 preprocessCore_1.20.0 splines_2.15.2 stats4_2.15.2 tools_2.15.2 [21] zlibbioc_1.4.0 [[alternative HTML version deleted]]
vsn oligo oligoclasses • 968 views
ADD COMMENTlink modified 6.9 years ago by James W. MacDonald51k • written 6.9 years ago by José LÓPEZ110
Answer: vsn preprocess with oligo package
0
gravatar for James W. MacDonald
6.9 years ago by
United States
James W. MacDonald51k wrote:
Hi Jose, Let's say you followed Benilton's code from https://stat.ethz.ch/pipermail/bioconductor/2010-June/033936.html library(oligo) cels = list.celfiles() raw = read.celfiles(cels) raw = backgroundCorrect(raw, "rma") ## I added this - you might want BG correction pms = pm(raw) pmsVSN = vsn::vsnMatrix(pms) pm(raw) <- pmVSN rm(pms, pmsVSN) you now have an ExpressionFeatureSet with normalized data that you want to summarize. You can then eset <- summarize(raw, method = "medianpolish") See ?summarizationMethods for more information. Best, Jim On 1/11/2013 6:17 AM, Jos? L?PEZ wrote: > Dear Benilton, > > I am using oligo for Mouse Gene 1.0ST arrays. In addition to RMA, I would also like to pre-process with vsn. I have seen previous threads related to this question in the past, (https://stat.ethz.ch/pipermail/bioconductor/2010-January/031100.html, https://stat.ethz.ch/pipermail/bioconductor/2010-June/033936.html), but unfortunately, I am not bioinformatician and, although I read oligo and vsn manuals, it is not easy to me to follow up to summarize the vsn object. > May you (or someone else) please, give me some additional clue to sumarize the vsn object using the oligo package. > > Thank you very much in advance for your time and your kind help, > > Jose LOPEZ > > ************************** > >> list.files() > [1] "ABRNA1.CEL" "ABRNA2.CEL" "ABRNA3.CEL" > [4] "ABRNA4.CEL" "ABRNA5.CEL" "ABRNA6.CEL" > [7] "Limma_FilterBefore_H2BGFP_jla_vsn.R" >> library(limma) >> library(oligo) > Loading required package: BiocGenerics > > Attaching package: ?BiocGenerics? > > The following object(s) are masked from ?package:stats?: > > xtabs > > The following object(s) are masked from ?package:base?: > > anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, > mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, > setdiff, table, tapply, union, unique > > Loading required package: oligoClasses > Loading package bit 1.1-9 > package:bit (c) 2008-2012 Jens Oehlschlaegel (GPL-2) > creators: bit bitwhich > coercion: as.logical as.integer as.bit as.bitwhich which > operator: !& | xor != == > querying: print length any all min max range sum summary > bit access: length<- [ [<- [[ [[<- > for more help type ?bit > Loading package ff2.2-10 > - getOption("fftempdir")=="/var/folders/U+/U+SFMmqcEbKkSysJQ3OYbk+++ TQ/-Tmp-//RtmpKgQzWD" > > - getOption("ffextension")=="ff" > > - getOption("ffdrop")==TRUE > > - getOption("fffinonexit")==TRUE > > - getOption("ffpagesize")==65536 > > - getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes > > - getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system > > - getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system > > Welcome to oligoClasses version 1.20.0 > Loading required package: Biobase > Welcome to Bioconductor > > Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see > 'citation("Biobase")', and for packages 'citation("pkgname")'. > > ==================================================================== ==================================================== > Welcome to oligo version 1.22.0 > ==================================================================== ==================================================== > > Attaching package: ?oligo? > > The following object(s) are masked from ?package:limma?: > > backgroundCorrect > >> Data=read.celfiles(list.celfiles()) > Loading required package: pd.mogene.1.0.st.v1 > Loading required package: RSQLite > Loading required package: DBI > Platform design info loaded. > Reading in : ABRNA1.CEL > Reading in : ABRNA2.CEL > Reading in : ABRNA3.CEL > Reading in : ABRNA4.CEL > Reading in : ABRNA5.CEL > Reading in : ABRNA6.CEL >> pms=pm(Data) >> class(pms) > [1] "matrix" >> head(pms) > ABRNA1.CEL ABRNA2.CEL ABRNA3.CEL ABRNA4.CEL ABRNA5.CEL ABRNA6.CEL > 2106 46 43 36 36 37 33 > 2107 38 32 33 36 43 34 > 2108 31 31 35 34 37 35 > 2109 54 46 45 40 58 35 > 2110 58 55 40 39 94 40 > 2111 53 39 34 36 43 43 >> pmsVSN=vsn::vsnMatrix(pms) > vsn2: 899636 x 6 matrix (1 stratum). Please use 'meanSdPlot' to verify the fit. >> class(pmsVSN) > [1] "vsn" > attr(,"package") > [1] "vsn" >> pmsVSN > vsn object for n=899636 features and d=6 samples. > sigsq=0.026 > hx: 899636 x 6 matrix. >> eset=rma(pmsVSN, background=FALSE,normalize=FALSE) > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function ?rma? for signature ?"vsn"? > >> library(vsn) >> meanSdPlot(pmsVSN) > KernSmooth 2.23 loaded > Copyright M. P. Wand 1997-2009 > >> sessionInfo() > R version 2.15.2 (2012-10-26) > Platform: i386-apple-darwin9.8.0/i386 (32-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] vsn_3.26.0 pd.mogene.1.0.st.v1_3.8.0 RSQLite_0.11.2 DBI_0.2-5 > [5] oligo_1.22.0 Biobase_2.18.0 oligoClasses_1.20.0 BiocGenerics_0.4.0 > [9] limma_3.14.3 > > loaded via a namespace (and not attached): > [1] affxparser_1.30.0 affy_1.36.0 affyio_1.26.0 BiocInstaller_1.8.3 Biostrings_2.26.2 > [6] bit_1.1-9 codetools_0.2-8 ff_2.2-10 foreach_1.4.0 GenomicRanges_1.10.5 > [11] grid_2.15.2 IRanges_1.16.4 iterators_1.0.6 KernSmooth_2.23-8 lattice_0.20-10 > [16] parallel_2.15.2 preprocessCore_1.20.0 splines_2.15.2 stats4_2.15.2 tools_2.15.2 > [21] zlibbioc_1.4.0 > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink written 6.9 years ago by James W. MacDonald51k
Dear Jim, Thank you for the advise on the background correction step. I already tryed before the whole Benilton's code but it doesn't work at the following step. > pm(raw) <- pmVSN Error: object 'pmVSN' not found May I ask you what this step is doing? Does it replace the pm matrix in the raw ExpressionFeatureSet by the normalized one? Thank you in advance for your time and your kind help, Jose > library(limma) > library(oligo) > Data=read.celfiles(list.celfiles()) Loading required package: pd.mogene.1.0.st.v1 Loading required package: RSQLite Loading required package: DBI Platform design info loaded. Reading in : ABRNA1.CEL Reading in : ABRNA2.CEL Reading in : ABRNA3.CEL Reading in : ABRNA4.CEL Reading in : ABRNA5.CEL Reading in : ABRNA6.CEL > pms=pm(Data) > raw=backgroundCorrect(Data,"rma") Background correcting... OK > pms=pm(raw) > pmsVSN=vsn::vsnMatrix(pms) vsn2: 899636 x 6 matrix (1 stratum). Please use 'meanSdPlot' to verify the fit. > pm(raw) <- pmVSN Error: object 'pmVSN' not found > pm(raw) <- pmsVSN Error in function (classes, fdef, mtable) : unable to find an inherited method for function ?pm<-? for signature ?"GeneFeatureSet", "missing", "missing", "vsn"? > pmsVSN vsn object for n=899636 features and d=6 samples. sigsq=0.1 hx: 899636 x 6 matrix. > head(pms) ABRNA1.CEL ABRNA2.CEL ABRNA3.CEL ABRNA4.CEL ABRNA5.CEL ABRNA6.CEL 2106 7.853059 7.635413 5.221570 5.160448 5.978796 5.767533 2107 5.990083 4.764031 4.659925 5.160448 7.067603 5.903628 2108 4.867173 4.587342 5.023095 4.762256 5.978796 6.045105 2109 10.657556 8.827158 7.679404 6.124607 11.523816 6.045105 2110 12.538396 13.906774 6.147958 5.860049 38.764281 6.843026 2111 10.241785 6.356910 4.836138 5.160448 7.067603 7.405633 > class(pms) [1] "matrix" > ls() [1] "Data" "pms" "pmsVSN" "raw" > sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pd.mogene.1.0.st.v1_3.8.0 RSQLite_0.11.2 DBI_0.2-5 oligo_1.22.0 [5] Biobase_2.18.0 oligoClasses_1.20.0 BiocGenerics_0.4.0 limma_3.14.3 loaded via a namespace (and not attached): [1] affxparser_1.30.0 affy_1.36.0 affyio_1.26.0 BiocInstaller_1.8.3 Biostrings_2.26.2 [6] bit_1.1-9 codetools_0.2-8 ff_2.2-10 foreach_1.4.0 GenomicRanges_1.10.5 [11] grid_2.15.2 IRanges_1.16.4 iterators_1.0.6 lattice_0.20-10 parallel_2.15.2 [16] preprocessCore_1.20.0 splines_2.15.2 stats4_2.15.2 vsn_3.26.0 zlibbioc_1.4.0 ***************************************************** Jos? P. L?PEZ-ATAYALA Instituto de Neurociencias CSIC - UMH Avda. D. Santiago Ram?n y Cajal, S/N E-03550, Sant Joan d'Alacant Alicante, Spain jose.lopez at umh.es http://in.umh.es/grupos-detalle.aspx?grupo=30 (34) 965 919 531 El ene 11, 2013, a las 3:59 p.m., James W. MacDonald escribi?: > Hi Jose, > > Let's say you followed Benilton's code from https://stat.ethz.ch/pipermail/bioconductor/2010-June/033936.html > > library(oligo) > cels = list.celfiles() > raw = read.celfiles(cels) > raw = backgroundCorrect(raw, "rma") ## I added this - you might want BG correction > pms = pm(raw) > pmsVSN = vsn::vsnMatrix(pms) > pm(raw) <- pmVSN > rm(pms, pmsVSN) > > you now have an ExpressionFeatureSet with normalized data that you want to summarize. You can then > > eset <- summarize(raw, method = "medianpolish") > > See > > ?summarizationMethods > > for more information. > > Best, > > Jim > > > On 1/11/2013 6:17 AM, Jos? L?PEZ wrote: >> Dear Benilton, >> >> I am using oligo for Mouse Gene 1.0ST arrays. In addition to RMA, I would also like to pre-process with vsn. I have seen previous threads related to this question in the past, (https://stat.ethz.ch/pipermail/bioconductor/2010-January/031100.html, https://stat.ethz.ch/pipermail/bioconductor/2010-June/033936.html), but unfortunately, I am not bioinformatician and, although I read oligo and vsn manuals, it is not easy to me to follow up to summarize the vsn object. >> May you (or someone else) please, give me some additional clue to sumarize the vsn object using the oligo package. >> >> Thank you very much in advance for your time and your kind help, >> >> Jose LOPEZ >> >> ************************** >> >>> list.files() >> [1] "ABRNA1.CEL" "ABRNA2.CEL" "ABRNA3.CEL" >> [4] "ABRNA4.CEL" "ABRNA5.CEL" "ABRNA6.CEL" >> [7] "Limma_FilterBefore_H2BGFP_jla_vsn.R" >>> library(limma) >>> library(oligo) >> Loading required package: BiocGenerics >> >> Attaching package: ?BiocGenerics? >> >> The following object(s) are masked from ?package:stats?: >> >> xtabs >> >> The following object(s) are masked from ?package:base?: >> >> anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, >> mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, >> setdiff, table, tapply, union, unique >> >> Loading required package: oligoClasses >> Loading package bit 1.1-9 >> package:bit (c) 2008-2012 Jens Oehlschlaegel (GPL-2) >> creators: bit bitwhich >> coercion: as.logical as.integer as.bit as.bitwhich which >> operator: !& | xor != == >> querying: print length any all min max range sum summary >> bit access: length<- [ [<- [[ [[<- >> for more help type ?bit >> Loading package ff2.2-10 >> - getOption("fftempdir")=="/var/folders/U+/U+SFMmqcEbKkSysJQ3OYbk++ +TQ/-Tmp-//RtmpKgQzWD" >> >> - getOption("ffextension")=="ff" >> >> - getOption("ffdrop")==TRUE >> >> - getOption("fffinonexit")==TRUE >> >> - getOption("ffpagesize")==65536 >> >> - getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes >> >> - getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system >> >> - getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system >> >> Welcome to oligoClasses version 1.20.0 >> Loading required package: Biobase >> Welcome to Bioconductor >> >> Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see >> 'citation("Biobase")', and for packages 'citation("pkgname")'. >> >> =================================================================== ===================================================== >> Welcome to oligo version 1.22.0 >> =================================================================== ===================================================== >> >> Attaching package: ?oligo? >> >> The following object(s) are masked from ?package:limma?: >> >> backgroundCorrect >> >>> Data=read.celfiles(list.celfiles()) >> Loading required package: pd.mogene.1.0.st.v1 >> Loading required package: RSQLite >> Loading required package: DBI >> Platform design info loaded. >> Reading in : ABRNA1.CEL >> Reading in : ABRNA2.CEL >> Reading in : ABRNA3.CEL >> Reading in : ABRNA4.CEL >> Reading in : ABRNA5.CEL >> Reading in : ABRNA6.CEL >>> pms=pm(Data) >>> class(pms) >> [1] "matrix" >>> head(pms) >> ABRNA1.CEL ABRNA2.CEL ABRNA3.CEL ABRNA4.CEL ABRNA5.CEL ABRNA6.CEL >> 2106 46 43 36 36 37 33 >> 2107 38 32 33 36 43 34 >> 2108 31 31 35 34 37 35 >> 2109 54 46 45 40 58 35 >> 2110 58 55 40 39 94 40 >> 2111 53 39 34 36 43 43 >>> pmsVSN=vsn::vsnMatrix(pms) >> vsn2: 899636 x 6 matrix (1 stratum). Please use 'meanSdPlot' to verify the fit. >>> class(pmsVSN) >> [1] "vsn" >> attr(,"package") >> [1] "vsn" >>> pmsVSN >> vsn object for n=899636 features and d=6 samples. >> sigsq=0.026 >> hx: 899636 x 6 matrix. >>> eset=rma(pmsVSN, background=FALSE,normalize=FALSE) >> Error in function (classes, fdef, mtable) : >> unable to find an inherited method for function ?rma? for signature ?"vsn"? >> >>> library(vsn) >>> meanSdPlot(pmsVSN) >> KernSmooth 2.23 loaded >> Copyright M. P. Wand 1997-2009 >> >>> sessionInfo() >> R version 2.15.2 (2012-10-26) >> Platform: i386-apple-darwin9.8.0/i386 (32-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] vsn_3.26.0 pd.mogene.1.0.st.v1_3.8.0 RSQLite_0.11.2 DBI_0.2-5 >> [5] oligo_1.22.0 Biobase_2.18.0 oligoClasses_1.20.0 BiocGenerics_0.4.0 >> [9] limma_3.14.3 >> >> loaded via a namespace (and not attached): >> [1] affxparser_1.30.0 affy_1.36.0 affyio_1.26.0 BiocInstaller_1.8.3 Biostrings_2.26.2 >> [6] bit_1.1-9 codetools_0.2-8 ff_2.2-10 foreach_1.4.0 GenomicRanges_1.10.5 >> [11] grid_2.15.2 IRanges_1.16.4 iterators_1.0.6 KernSmooth_2.23-8 lattice_0.20-10 >> [16] parallel_2.15.2 preprocessCore_1.20.0 splines_2.15.2 stats4_2.15.2 tools_2.15.2 >> [21] zlibbioc_1.4.0 >> >> >> [[alternative HTML version deleted]] >> >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 >
ADD REPLYlink written 6.9 years ago by José LÓPEZ110
Hi Jose, On 1/11/2013 10:31 AM, Jos? L?PEZ wrote: > Dear Jim, > > Thank you for the advise on the background correction step. > I already tryed before the whole Benilton's code but it doesn't work at the following step. > >> pm(raw)<- pmVSN > Error: object 'pmVSN' not found > > May I ask you what this step is doing? Does it replace the pm matrix in the raw ExpressionFeatureSet by the normalized one? Exactly. But the 'pm <-' function expects to be fed a matrix, and the pmsVSN isn't a matrix. Instead, it is a 'vsn' object, which is related to an ExpressionSet object. So you can extract the matrix of normalized data as usual, with exprs(): pm(raw) <- exprs(pmsVSN) and there was another error in my code, as summarize() won't work on a GeneFeatureSet object. Instead, you want to use rma(): eset <- rma(raw, normalize = FALSE, background = FALSE) Best, Jim > > Thank you in advance for your time and your kind help, > > Jose > >> library(limma) >> library(oligo) >> Data=read.celfiles(list.celfiles()) > Loading required package: pd.mogene.1.0.st.v1 > Loading required package: RSQLite > Loading required package: DBI > Platform design info loaded. > Reading in : ABRNA1.CEL > Reading in : ABRNA2.CEL > Reading in : ABRNA3.CEL > Reading in : ABRNA4.CEL > Reading in : ABRNA5.CEL > Reading in : ABRNA6.CEL >> pms=pm(Data) >> raw=backgroundCorrect(Data,"rma") > Background correcting... OK >> pms=pm(raw) >> pmsVSN=vsn::vsnMatrix(pms) > vsn2: 899636 x 6 matrix (1 stratum). Please use 'meanSdPlot' to verify the fit. >> pm(raw)<- pmVSN > Error: object 'pmVSN' not found >> pm(raw)<- pmsVSN > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function ?pm<-? for signature ?"GeneFeatureSet", "missing", "missing", "vsn"? >> pmsVSN > vsn object for n=899636 features and d=6 samples. > sigsq=0.1 > hx: 899636 x 6 matrix. >> head(pms) > ABRNA1.CEL ABRNA2.CEL ABRNA3.CEL ABRNA4.CEL ABRNA5.CEL ABRNA6.CEL > 2106 7.853059 7.635413 5.221570 5.160448 5.978796 5.767533 > 2107 5.990083 4.764031 4.659925 5.160448 7.067603 5.903628 > 2108 4.867173 4.587342 5.023095 4.762256 5.978796 6.045105 > 2109 10.657556 8.827158 7.679404 6.124607 11.523816 6.045105 > 2110 12.538396 13.906774 6.147958 5.860049 38.764281 6.843026 > 2111 10.241785 6.356910 4.836138 5.160448 7.067603 7.405633 >> class(pms) > [1] "matrix" >> ls() > [1] "Data" "pms" "pmsVSN" "raw" > >> sessionInfo() > R version 2.15.2 (2012-10-26) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] pd.mogene.1.0.st.v1_3.8.0 RSQLite_0.11.2 DBI_0.2-5 oligo_1.22.0 > [5] Biobase_2.18.0 oligoClasses_1.20.0 BiocGenerics_0.4.0 limma_3.14.3 > > loaded via a namespace (and not attached): > [1] affxparser_1.30.0 affy_1.36.0 affyio_1.26.0 BiocInstaller_1.8.3 Biostrings_2.26.2 > [6] bit_1.1-9 codetools_0.2-8 ff_2.2-10 foreach_1.4.0 GenomicRanges_1.10.5 > [11] grid_2.15.2 IRanges_1.16.4 iterators_1.0.6 lattice_0.20-10 parallel_2.15.2 > [16] preprocessCore_1.20.0 splines_2.15.2 stats4_2.15.2 vsn_3.26.0 zlibbioc_1.4.0 > > > ***************************************************** > Jos? P. L?PEZ-ATAYALA > Instituto de Neurociencias > CSIC - UMH > Avda. D. Santiago Ram?n y Cajal, S/N > E-03550, Sant Joan d'Alacant > Alicante, Spain > jose.lopez at umh.es > http://in.umh.es/grupos-detalle.aspx?grupo=30 > (34) 965 919 531 > > El ene 11, 2013, a las 3:59 p.m., James W. MacDonald escribi?: > >> Hi Jose, >> >> Let's say you followed Benilton's code from https://stat.ethz.ch/pipermail/bioconductor/2010-June/033936.html >> >> library(oligo) >> cels = list.celfiles() >> raw = read.celfiles(cels) >> raw = backgroundCorrect(raw, "rma") ## I added this - you might want BG correction >> pms = pm(raw) >> pmsVSN = vsn::vsnMatrix(pms) >> pm(raw)<- pmVSN >> rm(pms, pmsVSN) >> >> you now have an ExpressionFeatureSet with normalized data that you want to summarize. You can then >> >> eset<- summarize(raw, method = "medianpolish") >> >> See >> >> ?summarizationMethods >> >> for more information. >> >> Best, >> >> Jim >> >> >> On 1/11/2013 6:17 AM, Jos? L?PEZ wrote: >>> Dear Benilton, >>> >>> I am using oligo for Mouse Gene 1.0ST arrays. In addition to RMA, I would also like to pre-process with vsn. I have seen previous threads related to this question in the past, (https://stat.ethz.ch/pipermail/bioconductor/2010-January/031100.html, https://stat.ethz.ch/pipermail/bioconductor/2010-June/033936.html), but unfortunately, I am not bioinformatician and, although I read oligo and vsn manuals, it is not easy to me to follow up to summarize the vsn object. >>> May you (or someone else) please, give me some additional clue to sumarize the vsn object using the oligo package. >>> >>> Thank you very much in advance for your time and your kind help, >>> >>> Jose LOPEZ >>> >>> ************************** >>> >>>> list.files() >>> [1] "ABRNA1.CEL" "ABRNA2.CEL" "ABRNA3.CEL" >>> [4] "ABRNA4.CEL" "ABRNA5.CEL" "ABRNA6.CEL" >>> [7] "Limma_FilterBefore_H2BGFP_jla_vsn.R" >>>> library(limma) >>>> library(oligo) >>> Loading required package: BiocGenerics >>> >>> Attaching package: ?BiocGenerics? >>> >>> The following object(s) are masked from ?package:stats?: >>> >>> xtabs >>> >>> The following object(s) are masked from ?package:base?: >>> >>> anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, >>> mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, >>> setdiff, table, tapply, union, unique >>> >>> Loading required package: oligoClasses >>> Loading package bit 1.1-9 >>> package:bit (c) 2008-2012 Jens Oehlschlaegel (GPL-2) >>> creators: bit bitwhich >>> coercion: as.logical as.integer as.bit as.bitwhich which >>> operator: !& | xor != == >>> querying: print length any all min max range sum summary >>> bit access: length<- [ [<- [[ [[<- >>> for more help type ?bit >>> Loading package ff2.2-10 >>> - getOption("fftempdir")=="/var/folders/U+/U+SFMmqcEbKkSysJQ3OYbk+ ++TQ/-Tmp-//RtmpKgQzWD" >>> >>> - getOption("ffextension")=="ff" >>> >>> - getOption("ffdrop")==TRUE >>> >>> - getOption("fffinonexit")==TRUE >>> >>> - getOption("ffpagesize")==65536 >>> >>> - getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes >>> >>> - getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system >>> >>> - getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system >>> >>> Welcome to oligoClasses version 1.20.0 >>> Loading required package: Biobase >>> Welcome to Bioconductor >>> >>> Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see >>> 'citation("Biobase")', and for packages 'citation("pkgname")'. >>> >>> ================================================================== ====================================================== >>> Welcome to oligo version 1.22.0 >>> ================================================================== ====================================================== >>> >>> Attaching package: ?oligo? >>> >>> The following object(s) are masked from ?package:limma?: >>> >>> backgroundCorrect >>> >>>> Data=read.celfiles(list.celfiles()) >>> Loading required package: pd.mogene.1.0.st.v1 >>> Loading required package: RSQLite >>> Loading required package: DBI >>> Platform design info loaded. >>> Reading in : ABRNA1.CEL >>> Reading in : ABRNA2.CEL >>> Reading in : ABRNA3.CEL >>> Reading in : ABRNA4.CEL >>> Reading in : ABRNA5.CEL >>> Reading in : ABRNA6.CEL >>>> pms=pm(Data) >>>> class(pms) >>> [1] "matrix" >>>> head(pms) >>> ABRNA1.CEL ABRNA2.CEL ABRNA3.CEL ABRNA4.CEL ABRNA5.CEL ABRNA6.CEL >>> 2106 46 43 36 36 37 33 >>> 2107 38 32 33 36 43 34 >>> 2108 31 31 35 34 37 35 >>> 2109 54 46 45 40 58 35 >>> 2110 58 55 40 39 94 40 >>> 2111 53 39 34 36 43 43 >>>> pmsVSN=vsn::vsnMatrix(pms) >>> vsn2: 899636 x 6 matrix (1 stratum). Please use 'meanSdPlot' to verify the fit. >>>> class(pmsVSN) >>> [1] "vsn" >>> attr(,"package") >>> [1] "vsn" >>>> pmsVSN >>> vsn object for n=899636 features and d=6 samples. >>> sigsq=0.026 >>> hx: 899636 x 6 matrix. >>>> eset=rma(pmsVSN, background=FALSE,normalize=FALSE) >>> Error in function (classes, fdef, mtable) : >>> unable to find an inherited method for function ?rma? for signature ?"vsn"? >>> >>>> library(vsn) >>>> meanSdPlot(pmsVSN) >>> KernSmooth 2.23 loaded >>> Copyright M. P. Wand 1997-2009 >>> >>>> sessionInfo() >>> R version 2.15.2 (2012-10-26) >>> Platform: i386-apple-darwin9.8.0/i386 (32-bit) >>> >>> locale: >>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] vsn_3.26.0 pd.mogene.1.0.st.v1_3.8.0 RSQLite_0.11.2 DBI_0.2-5 >>> [5] oligo_1.22.0 Biobase_2.18.0 oligoClasses_1.20.0 BiocGenerics_0.4.0 >>> [9] limma_3.14.3 >>> >>> loaded via a namespace (and not attached): >>> [1] affxparser_1.30.0 affy_1.36.0 affyio_1.26.0 BiocInstaller_1.8.3 Biostrings_2.26.2 >>> [6] bit_1.1-9 codetools_0.2-8 ff_2.2-10 foreach_1.4.0 GenomicRanges_1.10.5 >>> [11] grid_2.15.2 IRanges_1.16.4 iterators_1.0.6 KernSmooth_2.23-8 lattice_0.20-10 >>> [16] parallel_2.15.2 preprocessCore_1.20.0 splines_2.15.2 stats4_2.15.2 tools_2.15.2 >>> [21] zlibbioc_1.4.0 >>> >>> >>> [[alternative HTML version deleted]] >>> >>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> -- >> James W. MacDonald, M.S. >> Biostatistician >> University of Washington >> Environmental and Occupational Health Sciences >> 4225 Roosevelt Way NE, # 100 >> Seattle WA 98105-6099 >> -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD REPLYlink written 6.9 years ago by James W. MacDonald51k
Yes, the exprs() did the job and it is allowing me to combine vsn with oligo and Gene ST arrays. Thank you again for your kind help, Best, Jose > library(limma) > library(oligo) > Data=read.celfiles(list.celfiles()) Loading required package: pd.mogene.1.0.st.v1 Loading required package: RSQLite Loading required package: DBI Platform design info loaded. Reading in : ABRNA1.CEL Reading in : ABRNA2.CEL Reading in : ABRNA3.CEL Reading in : ABRNA4.CEL Reading in : ABRNA5.CEL Reading in : ABRNA6.CEL > Data GeneFeatureSet (storageMode: lockedEnvironment) assayData: 1102500 features, 6 samples element names: exprs protocolData rowNames: ABRNA1.CEL ABRNA2.CEL ... ABRNA6.CEL (6 total) varLabels: exprs dates varMetadata: labelDescription channel phenoData rowNames: ABRNA1.CEL ABRNA2.CEL ... ABRNA6.CEL (6 total) varLabels: index varMetadata: labelDescription channel featureData: none experimentData: use 'experimentData(object)' Annotation: pd.mogene.1.0.st.v1 > class(Data) [1] "GeneFeatureSet" attr(,"package") [1] "oligoClasses" > raw=backgroundCorrect(Data,"rma") Background correcting... OK > pms=pm(raw) > head(pms) ABRNA1.CEL ABRNA2.CEL ABRNA3.CEL ABRNA4.CEL ABRNA5.CEL ABRNA6.CEL 2106 7.853059 7.635413 5.221570 5.160448 5.978796 5.767533 2107 5.990083 4.764031 4.659925 5.160448 7.067603 5.903628 2108 4.867173 4.587342 5.023095 4.762256 5.978796 6.045105 2109 10.657556 8.827158 7.679404 6.124607 11.523816 6.045105 2110 12.538396 13.906774 6.147958 5.860049 38.764281 6.843026 2111 10.241785 6.356910 4.836138 5.160448 7.067603 7.405633 > class(pms) [1] "matrix" > pmsVSN=vsn::vsnMatrix(pms) vsn2: 899636 x 6 matrix (1 stratum). Please use 'meanSdPlot' to verify the fit. > class(pmsVSN) [1] "vsn" attr(,"package") [1] "vsn" > pmsVSN vsn object for n=899636 features and d=6 samples. sigsq=0.1 hx: 899636 x 6 matrix. > pm(raw) <- exprs(pmsVSN) > rm(pms, pmsVSN) > ls() [1] "Data" "raw" > raw GeneFeatureSet (storageMode: lockedEnvironment) assayData: 1102500 features, 6 samples element names: exprs protocolData rowNames: ABRNA1.CEL ABRNA2.CEL ... ABRNA6.CEL (6 total) varLabels: exprs dates varMetadata: labelDescription channel phenoData rowNames: ABRNA1.CEL ABRNA2.CEL ... ABRNA6.CEL (6 total) varLabels: index varMetadata: labelDescription channel featureData: none experimentData: use 'experimentData(object)' Annotation: pd.mogene.1.0.st.v1 > eset=rma(raw, background=FALSE,normalize=FALSE) Calculating Expression > eset ExpressionSet (storageMode: lockedEnvironment) assayData: 35556 features, 6 samples element names: exprs protocolData rowNames: ABRNA1.CEL ABRNA2.CEL ... ABRNA6.CEL (6 total) varLabels: exprs dates varMetadata: labelDescription channel phenoData rowNames: ABRNA1.CEL ABRNA2.CEL ... ABRNA6.CEL (6 total) varLabels: index varMetadata: labelDescription channel featureData: none experimentData: use 'experimentData(object)' Annotation: pd.mogene.1.0.st.v1 El ene 11, 2013, a las 5:07 p.m., James W. MacDonald escribió: > Hi Jose, > > On 1/11/2013 10:31 AM, José LÓPEZ wrote: >> Dear Jim, >> >> Thank you for the advise on the background correction step. >> I already tryed before the whole Benilton's code but it doesn't work at the following step. >> >>> pm(raw)<- pmVSN >> Error: object 'pmVSN' not found >> >> May I ask you what this step is doing? Does it replace the pm matrix in the raw ExpressionFeatureSet by the normalized one? > > Exactly. But the 'pm <-' function expects to be fed a matrix, and the pmsVSN isn't a matrix. Instead, it is a 'vsn' object, which is related to an ExpressionSet object. So you can extract the matrix of normalized data as usual, with exprs(): > > pm(raw) <- exprs(pmsVSN) > > and there was another error in my code, as summarize() won't work on a GeneFeatureSet object. Instead, you want to use rma(): > > eset <- rma(raw, normalize = FALSE, background = FALSE) > > Best, > > Jim > > > >> >> Thank you in advance for your time and your kind help, >> >> Jose >> >>> library(limma) >>> library(oligo) >>> Data=read.celfiles(list.celfiles()) >> Loading required package: pd.mogene.1.0.st.v1 >> Loading required package: RSQLite >> Loading required package: DBI >> Platform design info loaded. >> Reading in : ABRNA1.CEL >> Reading in : ABRNA2.CEL >> Reading in : ABRNA3.CEL >> Reading in : ABRNA4.CEL >> Reading in : ABRNA5.CEL >> Reading in : ABRNA6.CEL >>> pms=pm(Data) >>> raw=backgroundCorrect(Data,"rma") >> Background correcting... OK >>> pms=pm(raw) >>> pmsVSN=vsn::vsnMatrix(pms) >> vsn2: 899636 x 6 matrix (1 stratum). Please use 'meanSdPlot' to verify the fit. >>> pm(raw)<- pmVSN >> Error: object 'pmVSN' not found >>> pm(raw)<- pmsVSN >> Error in function (classes, fdef, mtable) : >> unable to find an inherited method for function ‘pm<-’ for signature ‘"GeneFeatureSet", "missing", "missing", "vsn"’ >>> pmsVSN >> vsn object for n=899636 features and d=6 samples. >> sigsq=0.1 >> hx: 899636 x 6 matrix. >>> head(pms) >> ABRNA1.CEL ABRNA2.CEL ABRNA3.CEL ABRNA4.CEL ABRNA5.CEL ABRNA6.CEL >> 2106 7.853059 7.635413 5.221570 5.160448 5.978796 5.767533 >> 2107 5.990083 4.764031 4.659925 5.160448 7.067603 5.903628 >> 2108 4.867173 4.587342 5.023095 4.762256 5.978796 6.045105 >> 2109 10.657556 8.827158 7.679404 6.124607 11.523816 6.045105 >> 2110 12.538396 13.906774 6.147958 5.860049 38.764281 6.843026 >> 2111 10.241785 6.356910 4.836138 5.160448 7.067603 7.405633 >>> class(pms) >> [1] "matrix" >>> ls() >> [1] "Data" "pms" "pmsVSN" "raw" >> >>> sessionInfo() >> R version 2.15.2 (2012-10-26) >> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] pd.mogene.1.0.st.v1_3.8.0 RSQLite_0.11.2 DBI_0.2-5 oligo_1.22.0 >> [5] Biobase_2.18.0 oligoClasses_1.20.0 BiocGenerics_0.4.0 limma_3.14.3 >> >> loaded via a namespace (and not attached): >> [1] affxparser_1.30.0 affy_1.36.0 affyio_1.26.0 BiocInstaller_1.8.3 Biostrings_2.26.2 >> [6] bit_1.1-9 codetools_0.2-8 ff_2.2-10 foreach_1.4.0 GenomicRanges_1.10.5 >> [11] grid_2.15.2 IRanges_1.16.4 iterators_1.0.6 lattice_0.20-10 parallel_2.15.2 >> [16] preprocessCore_1.20.0 splines_2.15.2 stats4_2.15.2 vsn_3.26.0 zlibbioc_1.4.0 >> >> >> ***************************************************** >> José P. LÓPEZ-ATAYALA >> Instituto de Neurociencias >> CSIC - UMH >> Avda. D. Santiago Ramón y Cajal, S/N >> E-03550, Sant Joan d'Alacant >> Alicante, Spain >> jose.lopez@umh.es >> http://in.umh.es/grupos-detalle.aspx?grupo=30 >> (34) 965 919 531 >> >> El ene 11, 2013, a las 3:59 p.m., James W. MacDonald escribió: >> >>> Hi Jose, >>> >>> Let's say you followed Benilton's code from https://stat.ethz.ch/pipermail/bioconductor/2010-June/033936.html >>> >>> library(oligo) >>> cels = list.celfiles() >>> raw = read.celfiles(cels) >>> raw = backgroundCorrect(raw, "rma") ## I added this - you might want BG correction >>> pms = pm(raw) >>> pmsVSN = vsn::vsnMatrix(pms) >>> pm(raw)<- pmVSN >>> rm(pms, pmsVSN) >>> >>> you now have an ExpressionFeatureSet with normalized data that you want to summarize. You can then >>> >>> eset<- summarize(raw, method = "medianpolish") >>> >>> See >>> >>> ?summarizationMethods >>> >>> for more information. >>> >>> Best, >>> >>> Jim >>> >>> >>> On 1/11/2013 6:17 AM, José LÓPEZ wrote: >>>> Dear Benilton, >>>> >>>> I am using oligo for Mouse Gene 1.0ST arrays. In addition to RMA, I would also like to pre-process with vsn. I have seen previous threads related to this question in the past, (https://stat.ethz.ch/pipermail/bioconductor/2010-January/031100.html, https://stat.ethz.ch/pipermail/bioconductor/2010-June/033936.html), but unfortunately, I am not bioinformatician and, although I read oligo and vsn manuals, it is not easy to me to follow up to summarize the vsn object. >>>> May you (or someone else) please, give me some additional clue to sumarize the vsn object using the oligo package. >>>> >>>> Thank you very much in advance for your time and your kind help, >>>> >>>> Jose LOPEZ >>>> >>>> ************************** >>>> >>>>> list.files() >>>> [1] "ABRNA1.CEL" "ABRNA2.CEL" "ABRNA3.CEL" >>>> [4] "ABRNA4.CEL" "ABRNA5.CEL" "ABRNA6.CEL" >>>> [7] "Limma_FilterBefore_H2BGFP_jla_vsn.R" >>>>> library(limma) >>>>> library(oligo) >>>> Loading required package: BiocGenerics >>>> >>>> Attaching package: ‘BiocGenerics’ >>>> >>>> The following object(s) are masked from ‘package:stats’: >>>> >>>> xtabs >>>> >>>> The following object(s) are masked from ‘package:base’: >>>> >>>> anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, >>>> mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, >>>> setdiff, table, tapply, union, unique >>>> >>>> Loading required package: oligoClasses >>>> Loading package bit 1.1-9 >>>> package:bit (c) 2008-2012 Jens Oehlschlaegel (GPL-2) >>>> creators: bit bitwhich >>>> coercion: as.logical as.integer as.bit as.bitwhich which >>>> operator: !& | xor != == >>>> querying: print length any all min max range sum summary >>>> bit access: length<- [ [<- [[ [[<- >>>> for more help type ?bit >>>> Loading package ff2.2-10 >>>> - getOption("fftempdir")=="/var/folders/U+/U+SFMmqcEbKkSysJQ3OYbk +++TQ/-Tmp-//RtmpKgQzWD" >>>> >>>> - getOption("ffextension")=="ff" >>>> >>>> - getOption("ffdrop")==TRUE >>>> >>>> - getOption("fffinonexit")==TRUE >>>> >>>> - getOption("ffpagesize")==65536 >>>> >>>> - getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes >>>> >>>> - getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system >>>> >>>> - getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system >>>> >>>> Welcome to oligoClasses version 1.20.0 >>>> Loading required package: Biobase >>>> Welcome to Bioconductor >>>> >>>> Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see >>>> 'citation("Biobase")', and for packages 'citation("pkgname")'. >>>> >>>> ================================================================= ======================================================= >>>> Welcome to oligo version 1.22.0 >>>> ================================================================= ======================================================= >>>> >>>> Attaching package: ‘oligo’ >>>> >>>> The following object(s) are masked from ‘package:limma’: >>>> >>>> backgroundCorrect >>>> >>>>> Data=read.celfiles(list.celfiles()) >>>> Loading required package: pd.mogene.1.0.st.v1 >>>> Loading required package: RSQLite >>>> Loading required package: DBI >>>> Platform design info loaded. >>>> Reading in : ABRNA1.CEL >>>> Reading in : ABRNA2.CEL >>>> Reading in : ABRNA3.CEL >>>> Reading in : ABRNA4.CEL >>>> Reading in : ABRNA5.CEL >>>> Reading in : ABRNA6.CEL >>>>> pms=pm(Data) >>>>> class(pms) >>>> [1] "matrix" >>>>> head(pms) >>>> ABRNA1.CEL ABRNA2.CEL ABRNA3.CEL ABRNA4.CEL ABRNA5.CEL ABRNA6.CEL >>>> 2106 46 43 36 36 37 33 >>>> 2107 38 32 33 36 43 34 >>>> 2108 31 31 35 34 37 35 >>>> 2109 54 46 45 40 58 35 >>>> 2110 58 55 40 39 94 40 >>>> 2111 53 39 34 36 43 43 >>>>> pmsVSN=vsn::vsnMatrix(pms) >>>> vsn2: 899636 x 6 matrix (1 stratum). Please use 'meanSdPlot' to verify the fit. >>>>> class(pmsVSN) >>>> [1] "vsn" >>>> attr(,"package") >>>> [1] "vsn" >>>>> pmsVSN >>>> vsn object for n=899636 features and d=6 samples. >>>> sigsq=0.026 >>>> hx: 899636 x 6 matrix. >>>>> eset=rma(pmsVSN, background=FALSE,normalize=FALSE) >>>> Error in function (classes, fdef, mtable) : >>>> unable to find an inherited method for function ‘rma’ for signature ‘"vsn"’ >>>> >>>>> library(vsn) >>>>> meanSdPlot(pmsVSN) >>>> KernSmooth 2.23 loaded >>>> Copyright M. P. Wand 1997-2009 >>>> >>>>> sessionInfo() >>>> R version 2.15.2 (2012-10-26) >>>> Platform: i386-apple-darwin9.8.0/i386 (32-bit) >>>> >>>> locale: >>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> other attached packages: >>>> [1] vsn_3.26.0 pd.mogene.1.0.st.v1_3.8.0 RSQLite_0.11.2 DBI_0.2-5 >>>> [5] oligo_1.22.0 Biobase_2.18.0 oligoClasses_1.20.0 BiocGenerics_0.4.0 >>>> [9] limma_3.14.3 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] affxparser_1.30.0 affy_1.36.0 affyio_1.26.0 BiocInstaller_1.8.3 Biostrings_2.26.2 >>>> [6] bit_1.1-9 codetools_0.2-8 ff_2.2-10 foreach_1.4.0 GenomicRanges_1.10.5 >>>> [11] grid_2.15.2 IRanges_1.16.4 iterators_1.0.6 KernSmooth_2.23-8 lattice_0.20-10 >>>> [16] parallel_2.15.2 preprocessCore_1.20.0 splines_2.15.2 stats4_2.15.2 tools_2.15.2 >>>> [21] zlibbioc_1.4.0 >>>> >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor@r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> -- >>> James W. MacDonald, M.S. >>> Biostatistician >>> University of Washington >>> Environmental and Occupational Health Sciences >>> 4225 Roosevelt Way NE, # 100 >>> Seattle WA 98105-6099 >>> > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > [[alternative HTML version deleted]]
ADD REPLYlink written 6.9 years ago by José LÓPEZ110
Hi, I have one more question. The GeneFeatureSet has 1102500 features while the vsn2 is done on 899636 features no matter whether target in pm is "core" (default method) or "probeset". Why vsn2 does not use all the features? Is that correct/normal? After sumarization, as expected, I have 35556 features. It is possible that the normalization on only part of the features can introduce some kind of bias in the summarization process (899636 in stead of 1102500)? I think the alternative to this option is i.e. make the CDF file and environment (to avoid the unofficial CDF) and make vsnrma in affy but, since oligo was designed ad hoc (to analyze Gene and Exon affymetrix arrays), I though it makes sense to try to find your help to combine vsn and oligo. Thank you for your answer, Jose El ene 11, 2013, a las 5:42 p.m., José LÓPEZ escribió: > Yes, the exprs() did the job and it is allowing me to combine vsn with oligo and Gene ST arrays. > > Thank you again for your kind help, > > Best, > > Jose > > > > library(limma) > > library(oligo) > > Data=read.celfiles(list.celfiles()) > Loading required package: pd.mogene.1.0.st.v1 > Loading required package: RSQLite > Loading required package: DBI > Platform design info loaded. > Reading in : ABRNA1.CEL > Reading in : ABRNA2.CEL > Reading in : ABRNA3.CEL > Reading in : ABRNA4.CEL > Reading in : ABRNA5.CEL > Reading in : ABRNA6.CEL > > Data > GeneFeatureSet (storageMode: lockedEnvironment) > assayData: 1102500 features, 6 samples > element names: exprs > protocolData > rowNames: ABRNA1.CEL ABRNA2.CEL ... ABRNA6.CEL (6 total) > varLabels: exprs dates > varMetadata: labelDescription channel > phenoData > rowNames: ABRNA1.CEL ABRNA2.CEL ... ABRNA6.CEL (6 total) > varLabels: index > varMetadata: labelDescription channel > featureData: none > experimentData: use 'experimentData(object)' > Annotation: pd.mogene.1.0.st.v1 > > class(Data) > [1] "GeneFeatureSet" > attr(,"package") > [1] "oligoClasses" > > raw=backgroundCorrect(Data,"rma") > Background correcting... OK > > pms=pm(raw) > > head(pms) > ABRNA1.CEL ABRNA2.CEL ABRNA3.CEL ABRNA4.CEL ABRNA5.CEL ABRNA6.CEL > 2106 7.853059 7.635413 5.221570 5.160448 5.978796 5.767533 > 2107 5.990083 4.764031 4.659925 5.160448 7.067603 5.903628 > 2108 4.867173 4.587342 5.023095 4.762256 5.978796 6.045105 > 2109 10.657556 8.827158 7.679404 6.124607 11.523816 6.045105 > 2110 12.538396 13.906774 6.147958 5.860049 38.764281 6.843026 > 2111 10.241785 6.356910 4.836138 5.160448 7.067603 7.405633 > > class(pms) > [1] "matrix" > > pmsVSN=vsn::vsnMatrix(pms) > vsn2: 899636 x 6 matrix (1 stratum). Please use 'meanSdPlot' to verify the fit. > > class(pmsVSN) > [1] "vsn" > attr(,"package") > [1] "vsn" > > pmsVSN > vsn object for n=899636 features and d=6 samples. > sigsq=0.1 > hx: 899636 x 6 matrix. > > pm(raw) <- exprs(pmsVSN) > > rm(pms, pmsVSN) > > ls() > [1] "Data" "raw" > > raw > GeneFeatureSet (storageMode: lockedEnvironment) > assayData: 1102500 features, 6 samples > element names: exprs > protocolData > rowNames: ABRNA1.CEL ABRNA2.CEL ... ABRNA6.CEL (6 total) > varLabels: exprs dates > varMetadata: labelDescription channel > phenoData > rowNames: ABRNA1.CEL ABRNA2.CEL ... ABRNA6.CEL (6 total) > varLabels: index > varMetadata: labelDescription channel > featureData: none > experimentData: use 'experimentData(object)' > Annotation: pd.mogene.1.0.st.v1 > > eset=rma(raw, background=FALSE,normalize=FALSE) > Calculating Expression > > eset > ExpressionSet (storageMode: lockedEnvironment) > assayData: 35556 features, 6 samples > element names: exprs > protocolData > rowNames: ABRNA1.CEL ABRNA2.CEL ... ABRNA6.CEL (6 total) > varLabels: exprs dates > varMetadata: labelDescription channel > phenoData > rowNames: ABRNA1.CEL ABRNA2.CEL ... ABRNA6.CEL (6 total) > varLabels: index > varMetadata: labelDescription channel > featureData: none > experimentData: use 'experimentData(object)' > Annotation: pd.mogene.1.0.st.v1 > > El ene 11, 2013, a las 5:07 p.m., James W. MacDonald escribió: > >> Hi Jose, >> >> On 1/11/2013 10:31 AM, José LÓPEZ wrote: >>> Dear Jim, >>> >>> Thank you for the advise on the background correction step. >>> I already tryed before the whole Benilton's code but it doesn't work at the following step. >>> >>>> pm(raw)<- pmVSN >>> Error: object 'pmVSN' not found >>> >>> May I ask you what this step is doing? Does it replace the pm matrix in the raw ExpressionFeatureSet by the normalized one? >> >> Exactly. But the 'pm <-' function expects to be fed a matrix, and the pmsVSN isn't a matrix. Instead, it is a 'vsn' object, which is related to an ExpressionSet object. So you can extract the matrix of normalized data as usual, with exprs(): >> >> pm(raw) <- exprs(pmsVSN) >> >> and there was another error in my code, as summarize() won't work on a GeneFeatureSet object. Instead, you want to use rma(): >> >> eset <- rma(raw, normalize = FALSE, background = FALSE) >> >> Best, >> >> Jim >> >> >> >>> >>> Thank you in advance for your time and your kind help, >>> >>> Jose >>> >>>> library(limma) >>>> library(oligo) >>>> Data=read.celfiles(list.celfiles()) >>> Loading required package: pd.mogene.1.0.st.v1 >>> Loading required package: RSQLite >>> Loading required package: DBI >>> Platform design info loaded. >>> Reading in : ABRNA1.CEL >>> Reading in : ABRNA2.CEL >>> Reading in : ABRNA3.CEL >>> Reading in : ABRNA4.CEL >>> Reading in : ABRNA5.CEL >>> Reading in : ABRNA6.CEL >>>> pms=pm(Data) >>>> raw=backgroundCorrect(Data,"rma") >>> Background correcting... OK >>>> pms=pm(raw) >>>> pmsVSN=vsn::vsnMatrix(pms) >>> vsn2: 899636 x 6 matrix (1 stratum). Please use 'meanSdPlot' to verify the fit. >>>> pm(raw)<- pmVSN >>> Error: object 'pmVSN' not found >>>> pm(raw)<- pmsVSN >>> Error in function (classes, fdef, mtable) : >>> unable to find an inherited method for function ‘pm<-’ for signature ‘"GeneFeatureSet", "missing", "missing", "vsn"’ >>>> pmsVSN >>> vsn object for n=899636 features and d=6 samples. >>> sigsq=0.1 >>> hx: 899636 x 6 matrix. >>>> head(pms) >>> ABRNA1.CEL ABRNA2.CEL ABRNA3.CEL ABRNA4.CEL ABRNA5.CEL ABRNA6.CEL >>> 2106 7.853059 7.635413 5.221570 5.160448 5.978796 5.767533 >>> 2107 5.990083 4.764031 4.659925 5.160448 7.067603 5.903628 >>> 2108 4.867173 4.587342 5.023095 4.762256 5.978796 6.045105 >>> 2109 10.657556 8.827158 7.679404 6.124607 11.523816 6.045105 >>> 2110 12.538396 13.906774 6.147958 5.860049 38.764281 6.843026 >>> 2111 10.241785 6.356910 4.836138 5.160448 7.067603 7.405633 >>>> class(pms) >>> [1] "matrix" >>>> ls() >>> [1] "Data" "pms" "pmsVSN" "raw" >>> >>>> sessionInfo() >>> R version 2.15.2 (2012-10-26) >>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>> >>> locale: >>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] pd.mogene.1.0.st.v1_3.8.0 RSQLite_0.11.2 DBI_0.2-5 oligo_1.22.0 >>> [5] Biobase_2.18.0 oligoClasses_1.20.0 BiocGenerics_0.4.0 limma_3.14.3 >>> >>> loaded via a namespace (and not attached): >>> [1] affxparser_1.30.0 affy_1.36.0 affyio_1.26.0 BiocInstaller_1.8.3 Biostrings_2.26.2 >>> [6] bit_1.1-9 codetools_0.2-8 ff_2.2-10 foreach_1.4.0 GenomicRanges_1.10.5 >>> [11] grid_2.15.2 IRanges_1.16.4 iterators_1.0.6 lattice_0.20-10 parallel_2.15.2 >>> [16] preprocessCore_1.20.0 splines_2.15.2 stats4_2.15.2 vsn_3.26.0 zlibbioc_1.4.0 >>> >>> >>> ***************************************************** >>> José P. LÓPEZ-ATAYALA >>> Instituto de Neurociencias >>> CSIC - UMH >>> Avda. D. Santiago Ramón y Cajal, S/N >>> E-03550, Sant Joan d'Alacant >>> Alicante, Spain >>> jose.lopez@umh.es >>> http://in.umh.es/grupos-detalle.aspx?grupo=30 >>> (34) 965 919 531 >>> >>> El ene 11, 2013, a las 3:59 p.m., James W. MacDonald escribió: >>> >>>> Hi Jose, >>>> >>>> Let's say you followed Benilton's code from https://stat.ethz.ch/pipermail/bioconductor/2010-June/033936.html >>>> >>>> library(oligo) >>>> cels = list.celfiles() >>>> raw = read.celfiles(cels) >>>> raw = backgroundCorrect(raw, "rma") ## I added this - you might want BG correction >>>> pms = pm(raw) >>>> pmsVSN = vsn::vsnMatrix(pms) >>>> pm(raw)<- pmVSN >>>> rm(pms, pmsVSN) >>>> >>>> you now have an ExpressionFeatureSet with normalized data that you want to summarize. You can then >>>> >>>> eset<- summarize(raw, method = "medianpolish") >>>> >>>> See >>>> >>>> ?summarizationMethods >>>> >>>> for more information. >>>> >>>> Best, >>>> >>>> Jim >>>> >>>> >>>> On 1/11/2013 6:17 AM, José LÓPEZ wrote: >>>>> Dear Benilton, >>>>> >>>>> I am using oligo for Mouse Gene 1.0ST arrays. In addition to RMA, I would also like to pre-process with vsn. I have seen previous threads related to this question in the past, (https://stat.ethz.ch/pipermail/bioconductor/2010-January/031100.html, https://stat.ethz.ch/pipermail/bioconductor/2010-June/033936.html), but unfortunately, I am not bioinformatician and, although I read oligo and vsn manuals, it is not easy to me to follow up to summarize the vsn object. >>>>> May you (or someone else) please, give me some additional clue to sumarize the vsn object using the oligo package. >>>>> >>>>> Thank you very much in advance for your time and your kind help, >>>>> >>>>> Jose LOPEZ >>>>> >>>>> ************************** >>>>> >>>>>> list.files() >>>>> [1] "ABRNA1.CEL" "ABRNA2.CEL" "ABRNA3.CEL" >>>>> [4] "ABRNA4.CEL" "ABRNA5.CEL" "ABRNA6.CEL" >>>>> [7] "Limma_FilterBefore_H2BGFP_jla_vsn.R" >>>>>> library(limma) >>>>>> library(oligo) >>>>> Loading required package: BiocGenerics >>>>> >>>>> Attaching package: ‘BiocGenerics’ >>>>> >>>>> The following object(s) are masked from ‘package:stats’: >>>>> >>>>> xtabs >>>>> >>>>> The following object(s) are masked from ‘package:base’: >>>>> >>>>> anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, >>>>> mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, >>>>> setdiff, table, tapply, union, unique >>>>> >>>>> Loading required package: oligoClasses >>>>> Loading package bit 1.1-9 >>>>> package:bit (c) 2008-2012 Jens Oehlschlaegel (GPL-2) >>>>> creators: bit bitwhich >>>>> coercion: as.logical as.integer as.bit as.bitwhich which >>>>> operator: !& | xor != == >>>>> querying: print length any all min max range sum summary >>>>> bit access: length<- [ [<- [[ [[<- >>>>> for more help type ?bit >>>>> Loading package ff2.2-10 >>>>> - getOption("fftempdir")=="/var/folders/U+/U+SFMmqcEbKkSysJQ3OYb k+++TQ/-Tmp-//RtmpKgQzWD" >>>>> >>>>> - getOption("ffextension")=="ff" >>>>> >>>>> - getOption("ffdrop")==TRUE >>>>> >>>>> - getOption("fffinonexit")==TRUE >>>>> >>>>> - getOption("ffpagesize")==65536 >>>>> >>>>> - getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes >>>>> >>>>> - getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system >>>>> >>>>> - getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system >>>>> >>>>> Welcome to oligoClasses version 1.20.0 >>>>> Loading required package: Biobase >>>>> Welcome to Bioconductor >>>>> >>>>> Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see >>>>> 'citation("Biobase")', and for packages 'citation("pkgname")'. >>>>> >>>>> ================================================================ ======================================================== >>>>> Welcome to oligo version 1.22.0 >>>>> ================================================================ ======================================================== >>>>> >>>>> Attaching package: ‘oligo’ >>>>> >>>>> The following object(s) are masked from ‘package:limma’: >>>>> >>>>> backgroundCorrect >>>>> >>>>>> Data=read.celfiles(list.celfiles()) >>>>> Loading required package: pd.mogene.1.0.st.v1 >>>>> Loading required package: RSQLite >>>>> Loading required package: DBI >>>>> Platform design info loaded. >>>>> Reading in : ABRNA1.CEL >>>>> Reading in : ABRNA2.CEL >>>>> Reading in : ABRNA3.CEL >>>>> Reading in : ABRNA4.CEL >>>>> Reading in : ABRNA5.CEL >>>>> Reading in : ABRNA6.CEL >>>>>> pms=pm(Data) >>>>>> class(pms) >>>>> [1] "matrix" >>>>>> head(pms) >>>>> ABRNA1.CEL ABRNA2.CEL ABRNA3.CEL ABRNA4.CEL ABRNA5.CEL ABRNA6.CEL >>>>> 2106 46 43 36 36 37 33 >>>>> 2107 38 32 33 36 43 34 >>>>> 2108 31 31 35 34 37 35 >>>>> 2109 54 46 45 40 58 35 >>>>> 2110 58 55 40 39 94 40 >>>>> 2111 53 39 34 36 43 43 >>>>>> pmsVSN=vsn::vsnMatrix(pms) >>>>> vsn2: 899636 x 6 matrix (1 stratum). Please use 'meanSdPlot' to verify the fit. >>>>>> class(pmsVSN) >>>>> [1] "vsn" >>>>> attr(,"package") >>>>> [1] "vsn" >>>>>> pmsVSN >>>>> vsn object for n=899636 features and d=6 samples. >>>>> sigsq=0.026 >>>>> hx: 899636 x 6 matrix. >>>>>> eset=rma(pmsVSN, background=FALSE,normalize=FALSE) >>>>> Error in function (classes, fdef, mtable) : >>>>> unable to find an inherited method for function ‘rma’ for signature ‘"vsn"’ >>>>> >>>>>> library(vsn) >>>>>> meanSdPlot(pmsVSN) >>>>> KernSmooth 2.23 loaded >>>>> Copyright M. P. Wand 1997-2009 >>>>> >>>>>> sessionInfo() >>>>> R version 2.15.2 (2012-10-26) >>>>> Platform: i386-apple-darwin9.8.0/i386 (32-bit) >>>>> >>>>> locale: >>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>>>> >>>>> attached base packages: >>>>> [1] stats graphics grDevices utils datasets methods base >>>>> >>>>> other attached packages: >>>>> [1] vsn_3.26.0 pd.mogene.1.0.st.v1_3.8.0 RSQLite_0.11.2 DBI_0.2-5 >>>>> [5] oligo_1.22.0 Biobase_2.18.0 oligoClasses_1.20.0 BiocGenerics_0.4.0 >>>>> [9] limma_3.14.3 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] affxparser_1.30.0 affy_1.36.0 affyio_1.26.0 BiocInstaller_1.8.3 Biostrings_2.26.2 >>>>> [6] bit_1.1-9 codetools_0.2-8 ff_2.2-10 foreach_1.4.0 GenomicRanges_1.10.5 >>>>> [11] grid_2.15.2 IRanges_1.16.4 iterators_1.0.6 KernSmooth_2.23-8 lattice_0.20-10 >>>>> [16] parallel_2.15.2 preprocessCore_1.20.0 splines_2.15.2 stats4_2.15.2 tools_2.15.2 >>>>> [21] zlibbioc_1.4.0 >>>>> >>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor@r-project.org >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> -- >>>> James W. MacDonald, M.S. >>>> Biostatistician >>>> University of Washington >>>> Environmental and Occupational Health Sciences >>>> 4225 Roosevelt Way NE, # 100 >>>> Seattle WA 98105-6099 >>>> >> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> University of Washington >> Environmental and Occupational Health Sciences >> 4225 Roosevelt Way NE, # 100 >> Seattle WA 98105-6099 >> > [[alternative HTML version deleted]]
ADD REPLYlink written 6.9 years ago by José LÓPEZ110
Hi Jose, On 1/11/2013 12:05 PM, Jos? L?PEZ wrote: > Hi, > > I have one more question. The GeneFeatureSet has 1102500 features > while the vsn2 is done on 899636 features no matter whether target in > pm is "core" (default method) or "probeset". Why vsn2 does not use all > the features? Is that correct/normal? After sumarization, as expected, > I have 35556 features. It is possible that the normalization on only > part of the features can introduce some kind of bias in the > summarization process (899636 in stead of 1102500)? I think you misunderstand a basic tenet of Affymetrix arrays. Not all features on an Affy array are used to measure expression of transcript. There are for instance thousands of features that go all the way around the outside of the array (the oligo-dT features) that are there only to help the scanner align itself to the chip. There are also two big blocks of features in the middle that are not measuring transcript either. You can see this if you do something like tmp <- log2(as.numeric(exprs(raw([,1])))) geom <- geometry(getPD(raw)) ## convert back to a matrix tmp <- matrix(tmp, ncol = geom[1], nrow = geom[2]) ## reorder because image() is weird tmp <- as.matrix(rev(as.data.frame(tmp))) image(tmp[1:100,1:100]) This shows the (still transposed) top left corner of the chip. The checkerboard in the corner, and all the features along the top and side are oligo-dT probes used to align. The chip name is made up of oligo- dT features (and blanks) as well and there primarily I suppose to look cool. If you just do image(tmp), you will see the big blocks in the middle of the array. Does that help? Best, Jim > > I think the alternative to this option is i.e. make the CDF file and > environment (to avoid the unofficial CDF) and make vsnrma in affy but, > since oligo was designed ad hoc (to analyze Gene and Exon affymetrix > arrays), I though it makes sense to try to find your help to combine > vsn and oligo. > > Thank you for your answer, > > Jose > > El ene 11, 2013, a las 5:42 p.m., Jos? L?PEZ escribi?: > >> Yes, the exprs() did the job and it is allowing me to combine vsn >> with oligo and Gene ST arrays. >> >> Thank you again for your kind help, >> >> Best, >> >> Jose >> >> >> > library(limma) >> > library(oligo) >> > Data=read.celfiles(list.celfiles()) >> Loading required package: pd.mogene.1.0.st.v1 >> Loading required package: RSQLite >> Loading required package: DBI >> Platform design info loaded. >> Reading in : ABRNA1.CEL >> Reading in : ABRNA2.CEL >> Reading in : ABRNA3.CEL >> Reading in : ABRNA4.CEL >> Reading in : ABRNA5.CEL >> Reading in : ABRNA6.CEL >> > Data >> GeneFeatureSet (storageMode: lockedEnvironment) >> assayData: 1102500 features, 6 samples >> element names: exprs >> protocolData >> rowNames: ABRNA1.CEL ABRNA2.CEL ... ABRNA6.CEL (6 total) >> varLabels: exprs dates >> varMetadata: labelDescription channel >> phenoData >> rowNames: ABRNA1.CEL ABRNA2.CEL ... ABRNA6.CEL (6 total) >> varLabels: index >> varMetadata: labelDescription channel >> featureData: none >> experimentData: use 'experimentData(object)' >> Annotation: pd.mogene.1.0.st.v1 >> > class(Data) >> [1] "GeneFeatureSet" >> attr(,"package") >> [1] "oligoClasses" >> > raw=backgroundCorrect(Data,"rma") >> Background correcting... OK >> > pms=pm(raw) >> > head(pms) >> ABRNA1.CEL ABRNA2.CEL ABRNA3.CEL ABRNA4.CEL ABRNA5.CEL ABRNA6.CEL >> 2106 7.853059 7.635413 5.221570 5.160448 5.978796 5.767533 >> 2107 5.990083 4.764031 4.659925 5.160448 7.067603 5.903628 >> 2108 4.867173 4.587342 5.023095 4.762256 5.978796 6.045105 >> 2109 10.657556 8.827158 7.679404 6.124607 11.523816 6.045105 >> 2110 12.538396 13.906774 6.147958 5.860049 38.764281 6.843026 >> 2111 10.241785 6.356910 4.836138 5.160448 7.067603 7.405633 >> > class(pms) >> [1] "matrix" >> > pmsVSN=vsn::vsnMatrix(pms) >> vsn2: 899636 x 6 matrix (1 stratum). Please use 'meanSdPlot' to >> verify the fit. >> > class(pmsVSN) >> [1] "vsn" >> attr(,"package") >> [1] "vsn" >> > pmsVSN >> vsn object for n=899636 features and d=6 samples. >> sigsq=0.1 >> hx: 899636 x 6 matrix. >> > pm(raw) <- exprs(pmsVSN) >> > rm(pms, pmsVSN) >> > ls() >> [1] "Data" "raw" >> > raw >> GeneFeatureSet (storageMode: lockedEnvironment) >> assayData: 1102500 features, 6 samples >> element names: exprs >> protocolData >> rowNames: ABRNA1.CEL ABRNA2.CEL ... ABRNA6.CEL (6 total) >> varLabels: exprs dates >> varMetadata: labelDescription channel >> phenoData >> rowNames: ABRNA1.CEL ABRNA2.CEL ... ABRNA6.CEL (6 total) >> varLabels: index >> varMetadata: labelDescription channel >> featureData: none >> experimentData: use 'experimentData(object)' >> Annotation: pd.mogene.1.0.st.v1 >> > eset=rma(raw, background=FALSE,normalize=FALSE) >> Calculating Expression >> > eset >> ExpressionSet (storageMode: lockedEnvironment) >> assayData: 35556 features, 6 samples >> element names: exprs >> protocolData >> rowNames: ABRNA1.CEL ABRNA2.CEL ... ABRNA6.CEL (6 total) >> varLabels: exprs dates >> varMetadata: labelDescription channel >> phenoData >> rowNames: ABRNA1.CEL ABRNA2.CEL ... ABRNA6.CEL (6 total) >> varLabels: index >> varMetadata: labelDescription channel >> featureData: none >> experimentData: use 'experimentData(object)' >> Annotation: pd.mogene.1.0.st.v1 >> >> El ene 11, 2013, a las 5:07 p.m., James W. MacDonald escribi?: >> >>> Hi Jose, >>> >>> On 1/11/2013 10:31 AM, Jos? L?PEZ wrote: >>>> Dear Jim, >>>> >>>> Thank you for the advise on the background correction step. >>>> I already tryed before the whole Benilton's code but it doesn't >>>> work at the following step. >>>> >>>>> pm(raw)<- pmVSN >>>> Error: object 'pmVSN' not found >>>> >>>> May I ask you what this step is doing? Does it replace the pm >>>> matrix in the raw ExpressionFeatureSet by the normalized one? >>> >>> Exactly. But the 'pm <-' function expects to be fed a matrix, and >>> the pmsVSN isn't a matrix. Instead, it is a 'vsn' object, which is >>> related to an ExpressionSet object. So you can extract the matrix of >>> normalized data as usual, with exprs(): >>> >>> pm(raw) <- exprs(pmsVSN) >>> >>> and there was another error in my code, as summarize() won't work on >>> a GeneFeatureSet object. Instead, you want to use rma(): >>> >>> eset <- rma(raw, normalize = FALSE, background = FALSE) >>> >>> Best, >>> >>> Jim >>> >>> >>> >>>> >>>> Thank you in advance for your time and your kind help, >>>> >>>> Jose >>>> >>>>> library(limma) >>>>> library(oligo) >>>>> Data=read.celfiles(list.celfiles()) >>>> Loading required package: pd.mogene.1.0.st.v1 >>>> Loading required package: RSQLite >>>> Loading required package: DBI >>>> Platform design info loaded. >>>> Reading in : ABRNA1.CEL >>>> Reading in : ABRNA2.CEL >>>> Reading in : ABRNA3.CEL >>>> Reading in : ABRNA4.CEL >>>> Reading in : ABRNA5.CEL >>>> Reading in : ABRNA6.CEL >>>>> pms=pm(Data) >>>>> raw=backgroundCorrect(Data,"rma") >>>> Background correcting... OK >>>>> pms=pm(raw) >>>>> pmsVSN=vsn::vsnMatrix(pms) >>>> vsn2: 899636 x 6 matrix (1 stratum). Please use 'meanSdPlot' to >>>> verify the fit. >>>>> pm(raw)<- pmVSN >>>> Error: object 'pmVSN' not found >>>>> pm(raw)<- pmsVSN >>>> Error in function (classes, fdef, mtable) : >>>> unable to find an inherited method for function ?pm<-? for >>>> signature ?"GeneFeatureSet", "missing", "missing", "vsn"? >>>>> pmsVSN >>>> vsn object for n=899636 features and d=6 samples. >>>> sigsq=0.1 >>>> hx: 899636 x 6 matrix. >>>>> head(pms) >>>> ABRNA1.CEL ABRNA2.CEL ABRNA3.CEL ABRNA4.CEL ABRNA5.CEL ABRNA6.CEL >>>> 2106 7.853059 7.635413 5.221570 5.160448 5.978796 5.767533 >>>> 2107 5.990083 4.764031 4.659925 5.160448 7.067603 5.903628 >>>> 2108 4.867173 4.587342 5.023095 4.762256 5.978796 6.045105 >>>> 2109 10.657556 8.827158 7.679404 6.124607 11.523816 6.045105 >>>> 2110 12.538396 13.906774 6.147958 5.860049 38.764281 6.843026 >>>> 2111 10.241785 6.356910 4.836138 5.160448 7.067603 7.405633 >>>>> class(pms) >>>> [1] "matrix" >>>>> ls() >>>> [1] "Data" "pms" "pmsVSN" "raw" >>>> >>>>> sessionInfo() >>>> R version 2.15.2 (2012-10-26) >>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>>> >>>> locale: >>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> other attached packages: >>>> [1] pd.mogene.1.0.st.v1_3.8.0 RSQLite_0.11.2 DBI_0.2-5 >>>> oligo_1.22.0 >>>> [5] Biobase_2.18.0 oligoClasses_1.20.0 >>>> BiocGenerics_0.4.0 limma_3.14.3 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] affxparser_1.30.0 affy_1.36.0 affyio_1.26.0 >>>> BiocInstaller_1.8.3 Biostrings_2.26.2 >>>> [6] bit_1.1-9 codetools_0.2-8 ff_2.2-10 >>>> foreach_1.4.0 GenomicRanges_1.10.5 >>>> [11] grid_2.15.2 IRanges_1.16.4 iterators_1.0.6 >>>> lattice_0.20-10 parallel_2.15.2 >>>> [16] preprocessCore_1.20.0 splines_2.15.2 stats4_2.15.2 >>>> vsn_3.26.0 zlibbioc_1.4.0 >>>> >>>> >>>> ***************************************************** >>>> Jos? P. L?PEZ-ATAYALA >>>> Instituto de Neurociencias >>>> CSIC - UMH >>>> Avda. D. Santiago Ram?n y Cajal, S/N >>>> E-03550, Sant Joan d'Alacant >>>> Alicante, Spain >>>> jose.lopez at umh.es <mailto:jose.lopez at="" umh.es=""> >>>> http://in.umh.es/grupos-detalle.aspx?grupo=30 >>>> (34) 965 919 531 >>>> >>>> El ene 11, 2013, a las 3:59 p.m., James W. MacDonald escribi?: >>>> >>>>> Hi Jose, >>>>> >>>>> Let's say you followed Benilton's code from >>>>> https://stat.ethz.ch/pipermail/bioconductor/2010-June/033936.html >>>>> >>>>> library(oligo) >>>>> cels = list.celfiles() >>>>> raw = read.celfiles(cels) >>>>> raw = backgroundCorrect(raw, "rma") ## I added this - you might >>>>> want BG correction >>>>> pms = pm(raw) >>>>> pmsVSN = vsn::vsnMatrix(pms) >>>>> pm(raw)<- pmVSN >>>>> rm(pms, pmsVSN) >>>>> >>>>> you now have an ExpressionFeatureSet with normalized data that you >>>>> want to summarize. You can then >>>>> >>>>> eset<- summarize(raw, method = "medianpolish") >>>>> >>>>> See >>>>> >>>>> ?summarizationMethods >>>>> >>>>> for more information. >>>>> >>>>> Best, >>>>> >>>>> Jim >>>>> >>>>> >>>>> On 1/11/2013 6:17 AM, Jos? L?PEZ wrote: >>>>>> Dear Benilton, >>>>>> >>>>>> I am using oligo for Mouse Gene 1.0ST arrays. In addition to RMA, >>>>>> I would also like to pre-process with vsn. I have seen previous >>>>>> threads related to this question in the past, >>>>>> (https://stat.ethz.ch/pipermail/bioconductor/2010-January/031100.html, >>>>>> https://stat.ethz.ch/pipermail/bioconductor/2010-June/033936.html), >>>>>> but unfortunately, I am not bioinformatician and, although I read >>>>>> oligo and vsn manuals, it is not easy to me to follow up to >>>>>> summarize the vsn object. >>>>>> May you (or someone else) please, give me some additional clue to >>>>>> sumarize the vsn object using the oligo package. >>>>>> >>>>>> Thank you very much in advance for your time and your kind help, >>>>>> >>>>>> Jose LOPEZ >>>>>> >>>>>> ************************** >>>>>> >>>>>>> list.files() >>>>>> [1] "ABRNA1.CEL" "ABRNA2.CEL" >>>>>> "ABRNA3.CEL" >>>>>> [4] "ABRNA4.CEL" "ABRNA5.CEL" >>>>>> "ABRNA6.CEL" >>>>>> [7] "Limma_FilterBefore_H2BGFP_jla_vsn.R" >>>>>>> library(limma) >>>>>>> library(oligo) >>>>>> Loading required package: BiocGenerics >>>>>> >>>>>> Attaching package: ?BiocGenerics? >>>>>> >>>>>> The following object(s) are masked from ?package:stats?: >>>>>> >>>>>> xtabs >>>>>> >>>>>> The following object(s) are masked from ?package:base?: >>>>>> >>>>>> anyDuplicated, cbind, colnames, duplicated, eval, Filter, >>>>>> Find, get, intersect, lapply, Map, mapply, >>>>>> mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, >>>>>> rbind, Reduce, rep.int, rownames, sapply, >>>>>> setdiff, table, tapply, union, unique >>>>>> >>>>>> Loading required package: oligoClasses >>>>>> Loading package bit 1.1-9 >>>>>> package:bit (c) 2008-2012 Jens Oehlschlaegel (GPL-2) >>>>>> creators: bit bitwhich >>>>>> coercion: as.logical as.integer as.bit as.bitwhich which >>>>>> operator: !& | xor != == >>>>>> querying: print length any all min max range sum summary >>>>>> bit access: length<- [ [<- [[ [[<- >>>>>> for more help type ?bit >>>>>> Loading package ff2.2-10 >>>>>> - >>>>>> getOption("fftempdir")=="/var/folders/U+/U+SFMmqcEbKkSysJQ3OYbk +++TQ/-Tmp-//RtmpKgQzWD" >>>>>> >>>>>> - getOption("ffextension")=="ff" >>>>>> >>>>>> - getOption("ffdrop")==TRUE >>>>>> >>>>>> - getOption("fffinonexit")==TRUE >>>>>> >>>>>> - getOption("ffpagesize")==65536 >>>>>> >>>>>> - getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" >>>>>> if your system stalls on large writes >>>>>> >>>>>> - getOption("ffbatchbytes")==16777216 -- consider a different >>>>>> value for tuning your system >>>>>> >>>>>> - getOption("ffmaxbytes")==536870912 -- consider a different >>>>>> value for tuning your system >>>>>> >>>>>> Welcome to oligoClasses version 1.20.0 >>>>>> Loading required package: Biobase >>>>>> Welcome to Bioconductor >>>>>> >>>>>> Vignettes contain introductory material; view with >>>>>> 'browseVignettes()'. To cite Bioconductor, see >>>>>> 'citation("Biobase")', and for packages 'citation("pkgname")'. >>>>>> >>>>>> =============================================================== ========================================================= >>>>>> Welcome to oligo version 1.22.0 >>>>>> =============================================================== ========================================================= >>>>>> >>>>>> Attaching package: ?oligo? >>>>>> >>>>>> The following object(s) are masked from ?package:limma?: >>>>>> >>>>>> backgroundCorrect >>>>>> >>>>>>> Data=read.celfiles(list.celfiles()) >>>>>> Loading required package: pd.mogene.1.0.st.v1 >>>>>> Loading required package: RSQLite >>>>>> Loading required package: DBI >>>>>> Platform design info loaded. >>>>>> Reading in : ABRNA1.CEL >>>>>> Reading in : ABRNA2.CEL >>>>>> Reading in : ABRNA3.CEL >>>>>> Reading in : ABRNA4.CEL >>>>>> Reading in : ABRNA5.CEL >>>>>> Reading in : ABRNA6.CEL >>>>>>> pms=pm(Data) >>>>>>> class(pms) >>>>>> [1] "matrix" >>>>>>> head(pms) >>>>>> ABRNA1.CEL ABRNA2.CEL ABRNA3.CEL ABRNA4.CEL ABRNA5.CEL >>>>>> ABRNA6.CEL >>>>>> 2106 46 43 36 36 37 >>>>>> 33 >>>>>> 2107 38 32 33 36 43 >>>>>> 34 >>>>>> 2108 31 31 35 34 37 >>>>>> 35 >>>>>> 2109 54 46 45 40 58 >>>>>> 35 >>>>>> 2110 58 55 40 39 94 >>>>>> 40 >>>>>> 2111 53 39 34 36 43 >>>>>> 43 >>>>>>> pmsVSN=vsn::vsnMatrix(pms) >>>>>> vsn2: 899636 x 6 matrix (1 stratum). Please use 'meanSdPlot' to >>>>>> verify the fit. >>>>>>> class(pmsVSN) >>>>>> [1] "vsn" >>>>>> attr(,"package") >>>>>> [1] "vsn" >>>>>>> pmsVSN >>>>>> vsn object for n=899636 features and d=6 samples. >>>>>> sigsq=0.026 >>>>>> hx: 899636 x 6 matrix. >>>>>>> eset=rma(pmsVSN, background=FALSE,normalize=FALSE) >>>>>> Error in function (classes, fdef, mtable) : >>>>>> unable to find an inherited method for function ?rma? for >>>>>> signature ?"vsn"? >>>>>> >>>>>>> library(vsn) >>>>>>> meanSdPlot(pmsVSN) >>>>>> KernSmooth 2.23 loaded >>>>>> Copyright M. P. Wand 1997-2009 >>>>>> >>>>>>> sessionInfo() >>>>>> R version 2.15.2 (2012-10-26) >>>>>> Platform: i386-apple-darwin9.8.0/i386 (32-bit) >>>>>> >>>>>> locale: >>>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>>>>> >>>>>> attached base packages: >>>>>> [1] stats graphics grDevices utils datasets methods base >>>>>> >>>>>> other attached packages: >>>>>> [1] vsn_3.26.0 pd.mogene.1.0.st.v1_3.8.0 >>>>>> RSQLite_0.11.2 DBI_0.2-5 >>>>>> [5] oligo_1.22.0 Biobase_2.18.0 >>>>>> oligoClasses_1.20.0 BiocGenerics_0.4.0 >>>>>> [9] limma_3.14.3 >>>>>> >>>>>> loaded via a namespace (and not attached): >>>>>> [1] affxparser_1.30.0 affy_1.36.0 affyio_1.26.0 >>>>>> BiocInstaller_1.8.3 Biostrings_2.26.2 >>>>>> [6] bit_1.1-9 codetools_0.2-8 ff_2.2-10 >>>>>> foreach_1.4.0 GenomicRanges_1.10.5 >>>>>> [11] grid_2.15.2 IRanges_1.16.4 iterators_1.0.6 >>>>>> KernSmooth_2.23-8 lattice_0.20-10 >>>>>> [16] parallel_2.15.2 preprocessCore_1.20.0 splines_2.15.2 >>>>>> stats4_2.15.2 tools_2.15.2 >>>>>> [21] zlibbioc_1.4.0 >>>>>> >>>>>> >>>>>> [[alternative HTML version deleted]] >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Bioconductor mailing list >>>>>> Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> >>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>> Search the archives: >>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>> -- >>>>> James W. MacDonald, M.S. >>>>> Biostatistician >>>>> University of Washington >>>>> Environmental and Occupational Health Sciences >>>>> 4225 Roosevelt Way NE, # 100 >>>>> Seattle WA 98105-6099 >>>>> >>> >>> -- >>> James W. MacDonald, M.S. >>> Biostatistician >>> University of Washington >>> Environmental and Occupational Health Sciences >>> 4225 Roosevelt Way NE, # 100 >>> Seattle WA 98105-6099 >>> >> > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD REPLYlink written 6.9 years ago by James W. MacDonald51k
Ooops. Sorry for the question. I use to check CEL images and to further analyze quality with arrayQualityMetrics but yes, I didn't realize that the GeneFeatureSet was indicating the total number of probes in the array. Thank you again for your kind help, Best, Jose El ene 11, 2013, a las 6:46 p.m., James W. MacDonald escribi?: > Hi Jose, > > On 1/11/2013 12:05 PM, Jos? L?PEZ wrote: >> Hi, >> >> I have one more question. The GeneFeatureSet has 1102500 features >> while the vsn2 is done on 899636 features no matter whether target >> in pm is "core" (default method) or "probeset". Why vsn2 does not >> use all the features? Is that correct/normal? After sumarization, >> as expected, I have 35556 features. It is possible that the >> normalization on only part of the features can introduce some kind >> of bias in the summarization process (899636 in stead of 1102500)? > > I think you misunderstand a basic tenet of Affymetrix arrays. Not > all features on an Affy array are used to measure expression of > transcript. There are for instance thousands of features that go all > the way around the outside of the array (the oligo-dT features) that > are there only to help the scanner align itself to the chip. There > are also two big blocks of features in the middle that are not > measuring transcript either. > > You can see this if you do something like > > tmp <- log2(as.numeric(exprs(raw([,1])))) > geom <- geometry(getPD(raw)) > ## convert back to a matrix > tmp <- matrix(tmp, ncol = geom[1], nrow = geom[2]) > ## reorder because image() is weird > tmp <- as.matrix(rev(as.data.frame(tmp))) > image(tmp[1:100,1:100]) > > This shows the (still transposed) top left corner of the chip. The > checkerboard in the corner, and all the features along the top and > side are oligo-dT probes used to align. The chip name is made up of > oligo-dT features (and blanks) as well and there primarily I suppose > to look cool. > > If you just do image(tmp), you will see the big blocks in the middle > of the array. > > Does that help? > > Best, > > Jim > > > > >> >> I think the alternative to this option is i.e. make the CDF file >> and environment (to avoid the unofficial CDF) and make vsnrma in >> affy but, since oligo was designed ad hoc (to analyze Gene and Exon >> affymetrix arrays), I though it makes sense to try to find your >> help to combine vsn and oligo. >> >> Thank you for your answer, >> >> Jose >> >> El ene 11, 2013, a las 5:42 p.m., Jos? L?PEZ escribi?: >> >>> Yes, the exprs() did the job and it is allowing me to combine vsn >>> with oligo and Gene ST arrays. >>> >>> Thank you again for your kind help, >>> >>> Best, >>> >>> Jose >>> >>> >>> > library(limma) >>> > library(oligo) >>> > Data=read.celfiles(list.celfiles()) >>> Loading required package: pd.mogene.1.0.st.v1 >>> Loading required package: RSQLite >>> Loading required package: DBI >>> Platform design info loaded. >>> Reading in : ABRNA1.CEL >>> Reading in : ABRNA2.CEL >>> Reading in : ABRNA3.CEL >>> Reading in : ABRNA4.CEL >>> Reading in : ABRNA5.CEL >>> Reading in : ABRNA6.CEL >>> > Data >>> GeneFeatureSet (storageMode: lockedEnvironment) >>> assayData: 1102500 features, 6 samples >>> element names: exprs >>> protocolData >>> rowNames: ABRNA1.CEL ABRNA2.CEL ... ABRNA6.CEL (6 total) >>> varLabels: exprs dates >>> varMetadata: labelDescription channel >>> phenoData >>> rowNames: ABRNA1.CEL ABRNA2.CEL ... ABRNA6.CEL (6 total) >>> varLabels: index >>> varMetadata: labelDescription channel >>> featureData: none >>> experimentData: use 'experimentData(object)' >>> Annotation: pd.mogene.1.0.st.v1 >>> > class(Data) >>> [1] "GeneFeatureSet" >>> attr(,"package") >>> [1] "oligoClasses" >>> > raw=backgroundCorrect(Data,"rma") >>> Background correcting... OK >>> > pms=pm(raw) >>> > head(pms) >>> ABRNA1.CEL ABRNA2.CEL ABRNA3.CEL ABRNA4.CEL ABRNA5.CEL >>> ABRNA6.CEL >>> 2106 7.853059 7.635413 5.221570 5.160448 5.978796 >>> 5.767533 >>> 2107 5.990083 4.764031 4.659925 5.160448 7.067603 >>> 5.903628 >>> 2108 4.867173 4.587342 5.023095 4.762256 5.978796 >>> 6.045105 >>> 2109 10.657556 8.827158 7.679404 6.124607 11.523816 >>> 6.045105 >>> 2110 12.538396 13.906774 6.147958 5.860049 38.764281 >>> 6.843026 >>> 2111 10.241785 6.356910 4.836138 5.160448 7.067603 >>> 7.405633 >>> > class(pms) >>> [1] "matrix" >>> > pmsVSN=vsn::vsnMatrix(pms) >>> vsn2: 899636 x 6 matrix (1 stratum). Please use 'meanSdPlot' to >>> verify the fit. >>> > class(pmsVSN) >>> [1] "vsn" >>> attr(,"package") >>> [1] "vsn" >>> > pmsVSN >>> vsn object for n=899636 features and d=6 samples. >>> sigsq=0.1 >>> hx: 899636 x 6 matrix. >>> > pm(raw) <- exprs(pmsVSN) >>> > rm(pms, pmsVSN) >>> > ls() >>> [1] "Data" "raw" >>> > raw >>> GeneFeatureSet (storageMode: lockedEnvironment) >>> assayData: 1102500 features, 6 samples >>> element names: exprs >>> protocolData >>> rowNames: ABRNA1.CEL ABRNA2.CEL ... ABRNA6.CEL (6 total) >>> varLabels: exprs dates >>> varMetadata: labelDescription channel >>> phenoData >>> rowNames: ABRNA1.CEL ABRNA2.CEL ... ABRNA6.CEL (6 total) >>> varLabels: index >>> varMetadata: labelDescription channel >>> featureData: none >>> experimentData: use 'experimentData(object)' >>> Annotation: pd.mogene.1.0.st.v1 >>> > eset=rma(raw, background=FALSE,normalize=FALSE) >>> Calculating Expression >>> > eset >>> ExpressionSet (storageMode: lockedEnvironment) >>> assayData: 35556 features, 6 samples >>> element names: exprs >>> protocolData >>> rowNames: ABRNA1.CEL ABRNA2.CEL ... ABRNA6.CEL (6 total) >>> varLabels: exprs dates >>> varMetadata: labelDescription channel >>> phenoData >>> rowNames: ABRNA1.CEL ABRNA2.CEL ... ABRNA6.CEL (6 total) >>> varLabels: index >>> varMetadata: labelDescription channel >>> featureData: none >>> experimentData: use 'experimentData(object)' >>> Annotation: pd.mogene.1.0.st.v1 >>> >>> El ene 11, 2013, a las 5:07 p.m., James W. MacDonald escribi?: >>> >>>> Hi Jose, >>>> >>>> On 1/11/2013 10:31 AM, Jos? L?PEZ wrote: >>>>> Dear Jim, >>>>> >>>>> Thank you for the advise on the background correction step. >>>>> I already tryed before the whole Benilton's code but it doesn't >>>>> work at the following step. >>>>> >>>>>> pm(raw)<- pmVSN >>>>> Error: object 'pmVSN' not found >>>>> >>>>> May I ask you what this step is doing? Does it replace the pm >>>>> matrix in the raw ExpressionFeatureSet by the normalized one? >>>> >>>> Exactly. But the 'pm <-' function expects to be fed a matrix, >>>> and the pmsVSN isn't a matrix. Instead, it is a 'vsn' object, >>>> which is related to an ExpressionSet object. So you can extract >>>> the matrix of normalized data as usual, with exprs(): >>>> >>>> pm(raw) <- exprs(pmsVSN) >>>> >>>> and there was another error in my code, as summarize() won't work >>>> on a GeneFeatureSet object. Instead, you want to use rma(): >>>> >>>> eset <- rma(raw, normalize = FALSE, background = FALSE) >>>> >>>> Best, >>>> >>>> Jim >>>> >>>> >>>> >>>>> >>>>> Thank you in advance for your time and your kind help, >>>>> >>>>> Jose >>>>> >>>>>> library(limma) >>>>>> library(oligo) >>>>>> Data=read.celfiles(list.celfiles()) >>>>> Loading required package: pd.mogene.1.0.st.v1 >>>>> Loading required package: RSQLite >>>>> Loading required package: DBI >>>>> Platform design info loaded. >>>>> Reading in : ABRNA1.CEL >>>>> Reading in : ABRNA2.CEL >>>>> Reading in : ABRNA3.CEL >>>>> Reading in : ABRNA4.CEL >>>>> Reading in : ABRNA5.CEL >>>>> Reading in : ABRNA6.CEL >>>>>> pms=pm(Data) >>>>>> raw=backgroundCorrect(Data,"rma") >>>>> Background correcting... OK >>>>>> pms=pm(raw) >>>>>> pmsVSN=vsn::vsnMatrix(pms) >>>>> vsn2: 899636 x 6 matrix (1 stratum). Please use 'meanSdPlot' to >>>>> verify the fit. >>>>>> pm(raw)<- pmVSN >>>>> Error: object 'pmVSN' not found >>>>>> pm(raw)<- pmsVSN >>>>> Error in function (classes, fdef, mtable) : >>>>> unable to find an inherited method for function ?pm<-? for >>>>> signature ?"GeneFeatureSet", "missing", "missing", "vsn"? >>>>>> pmsVSN >>>>> vsn object for n=899636 features and d=6 samples. >>>>> sigsq=0.1 >>>>> hx: 899636 x 6 matrix. >>>>>> head(pms) >>>>> ABRNA1.CEL ABRNA2.CEL ABRNA3.CEL ABRNA4.CEL ABRNA5.CEL >>>>> ABRNA6.CEL >>>>> 2106 7.853059 7.635413 5.221570 5.160448 5.978796 >>>>> 5.767533 >>>>> 2107 5.990083 4.764031 4.659925 5.160448 7.067603 >>>>> 5.903628 >>>>> 2108 4.867173 4.587342 5.023095 4.762256 5.978796 >>>>> 6.045105 >>>>> 2109 10.657556 8.827158 7.679404 6.124607 11.523816 >>>>> 6.045105 >>>>> 2110 12.538396 13.906774 6.147958 5.860049 38.764281 >>>>> 6.843026 >>>>> 2111 10.241785 6.356910 4.836138 5.160448 7.067603 >>>>> 7.405633 >>>>>> class(pms) >>>>> [1] "matrix" >>>>>> ls() >>>>> [1] "Data" "pms" "pmsVSN" "raw" >>>>> >>>>>> sessionInfo() >>>>> R version 2.15.2 (2012-10-26) >>>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>>>> >>>>> locale: >>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>>>> >>>>> attached base packages: >>>>> [1] stats graphics grDevices utils datasets methods >>>>> base >>>>> >>>>> other attached packages: >>>>> [1] pd.mogene.1.0.st.v1_3.8.0 RSQLite_0.11.2 >>>>> DBI_0.2-5 oligo_1.22.0 >>>>> [5] Biobase_2.18.0 oligoClasses_1.20.0 >>>>> BiocGenerics_0.4.0 limma_3.14.3 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] affxparser_1.30.0 affy_1.36.0 >>>>> affyio_1.26.0 BiocInstaller_1.8.3 Biostrings_2.26.2 >>>>> [6] bit_1.1-9 codetools_0.2-8 >>>>> ff_2.2-10 foreach_1.4.0 GenomicRanges_1.10.5 >>>>> [11] grid_2.15.2 IRanges_1.16.4 >>>>> iterators_1.0.6 lattice_0.20-10 parallel_2.15.2 >>>>> [16] preprocessCore_1.20.0 splines_2.15.2 >>>>> stats4_2.15.2 vsn_3.26.0 zlibbioc_1.4.0 >>>>> >>>>> >>>>> ***************************************************** >>>>> Jos? P. L?PEZ-ATAYALA >>>>> Instituto de Neurociencias >>>>> CSIC - UMH >>>>> Avda. D. Santiago Ram?n y Cajal, S/N >>>>> E-03550, Sant Joan d'Alacant >>>>> Alicante, Spain >>>>> jose.lopez at umh.es <mailto:jose.lopez at="" umh.es=""> >>>>> http://in.umh.es/grupos-detalle.aspx?grupo=30 >>>>> (34) 965 919 531 >>>>> >>>>> El ene 11, 2013, a las 3:59 p.m., James W. MacDonald escribi?: >>>>> >>>>>> Hi Jose, >>>>>> >>>>>> Let's say you followed Benilton's code from https://stat.ethz.ch/pipermail/bioconductor/2010-June/033936.html >>>>>> >>>>>> library(oligo) >>>>>> cels = list.celfiles() >>>>>> raw = read.celfiles(cels) >>>>>> raw = backgroundCorrect(raw, "rma") ## I added this - you might >>>>>> want BG correction >>>>>> pms = pm(raw) >>>>>> pmsVSN = vsn::vsnMatrix(pms) >>>>>> pm(raw)<- pmVSN >>>>>> rm(pms, pmsVSN) >>>>>> >>>>>> you now have an ExpressionFeatureSet with normalized data that >>>>>> you want to summarize. You can then >>>>>> >>>>>> eset<- summarize(raw, method = "medianpolish") >>>>>> >>>>>> See >>>>>> >>>>>> ?summarizationMethods >>>>>> >>>>>> for more information. >>>>>> >>>>>> Best, >>>>>> >>>>>> Jim >>>>>> >>>>>> >>>>>> On 1/11/2013 6:17 AM, Jos? L?PEZ wrote: >>>>>>> Dear Benilton, >>>>>>> >>>>>>> I am using oligo for Mouse Gene 1.0ST arrays. In addition to >>>>>>> RMA, I would also like to pre-process with vsn. I have seen >>>>>>> previous threads related to this question in the past, (https://stat.ethz.ch/pipermail/bioconductor/2010-January/031100.html >>>>>>> , https://stat.ethz.ch/pipermail/bioconductor/2010-June/033936.html) >>>>>>> , but unfortunately, I am not bioinformatician and, although I >>>>>>> read oligo and vsn manuals, it is not easy to me to follow up >>>>>>> to summarize the vsn object. >>>>>>> May you (or someone else) please, give me some additional clue >>>>>>> to sumarize the vsn object using the oligo package. >>>>>>> >>>>>>> Thank you very much in advance for your time and your kind help, >>>>>>> >>>>>>> Jose LOPEZ >>>>>>> >>>>>>> ************************** >>>>>>> >>>>>>>> list.files() >>>>>>> [1] "ABRNA1.CEL" >>>>>>> "ABRNA2.CEL" "ABRNA3.CEL" >>>>>>> [4] "ABRNA4.CEL" >>>>>>> "ABRNA5.CEL" "ABRNA6.CEL" >>>>>>> [7] "Limma_FilterBefore_H2BGFP_jla_vsn.R" >>>>>>>> library(limma) >>>>>>>> library(oligo) >>>>>>> Loading required package: BiocGenerics >>>>>>> >>>>>>> Attaching package: ?BiocGenerics? >>>>>>> >>>>>>> The following object(s) are masked from ?package:stats?: >>>>>>> >>>>>>> xtabs >>>>>>> >>>>>>> The following object(s) are masked from ?package:base?: >>>>>>> >>>>>>> anyDuplicated, cbind, colnames, duplicated, eval, Filter, >>>>>>> Find, get, intersect, lapply, Map, mapply, >>>>>>> mget, order, paste, pmax, pmax.int, pmin, pmin.int, >>>>>>> Position, rbind, Reduce, rep.int, rownames, sapply, >>>>>>> setdiff, table, tapply, union, unique >>>>>>> >>>>>>> Loading required package: oligoClasses >>>>>>> Loading package bit 1.1-9 >>>>>>> package:bit (c) 2008-2012 Jens Oehlschlaegel (GPL-2) >>>>>>> creators: bit bitwhich >>>>>>> coercion: as.logical as.integer as.bit as.bitwhich which >>>>>>> operator: !& | xor != == >>>>>>> querying: print length any all min max range sum summary >>>>>>> bit access: length<- [ [<- [[ [[<- >>>>>>> for more help type ?bit >>>>>>> Loading package ff2.2-10 >>>>>>> - getOption("fftempdir")=="/var/folders/U+/U >>>>>>> +SFMmqcEbKkSysJQ3OYbk+++TQ/-Tmp-//RtmpKgQzWD" >>>>>>> >>>>>>> - getOption("ffextension")=="ff" >>>>>>> >>>>>>> - getOption("ffdrop")==TRUE >>>>>>> >>>>>>> - getOption("fffinonexit")==TRUE >>>>>>> >>>>>>> - getOption("ffpagesize")==65536 >>>>>>> >>>>>>> - getOption("ffcaching")=="mmnoflush" -- consider >>>>>>> "ffeachflush" if your system stalls on large writes >>>>>>> >>>>>>> - getOption("ffbatchbytes")==16777216 -- consider a different >>>>>>> value for tuning your system >>>>>>> >>>>>>> - getOption("ffmaxbytes")==536870912 -- consider a different >>>>>>> value for tuning your system >>>>>>> >>>>>>> Welcome to oligoClasses version 1.20.0 >>>>>>> Loading required package: Biobase >>>>>>> Welcome to Bioconductor >>>>>>> >>>>>>> Vignettes contain introductory material; view with >>>>>>> 'browseVignettes()'. To cite Bioconductor, see >>>>>>> 'citation("Biobase")', and for packages >>>>>>> 'citation("pkgname")'. >>>>>>> >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> ================================================================ >>>>>>> Welcome to oligo version 1.22.0 >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> = >>>>>>> ================================================================ >>>>>>> >>>>>>> Attaching package: ?oligo? >>>>>>> >>>>>>> The following object(s) are masked from ?package:limma?: >>>>>>> >>>>>>> backgroundCorrect >>>>>>> >>>>>>>> Data=read.celfiles(list.celfiles()) >>>>>>> Loading required package: pd.mogene.1.0.st.v1 >>>>>>> Loading required package: RSQLite >>>>>>> Loading required package: DBI >>>>>>> Platform design info loaded. >>>>>>> Reading in : ABRNA1.CEL >>>>>>> Reading in : ABRNA2.CEL >>>>>>> Reading in : ABRNA3.CEL >>>>>>> Reading in : ABRNA4.CEL >>>>>>> Reading in : ABRNA5.CEL >>>>>>> Reading in : ABRNA6.CEL >>>>>>>> pms=pm(Data) >>>>>>>> class(pms) >>>>>>> [1] "matrix" >>>>>>>> head(pms) >>>>>>> ABRNA1.CEL ABRNA2.CEL ABRNA3.CEL ABRNA4.CEL ABRNA5.CEL >>>>>>> ABRNA6.CEL >>>>>>> 2106 46 43 36 36 >>>>>>> 37 33 >>>>>>> 2107 38 32 33 36 >>>>>>> 43 34 >>>>>>> 2108 31 31 35 34 >>>>>>> 37 35 >>>>>>> 2109 54 46 45 40 >>>>>>> 58 35 >>>>>>> 2110 58 55 40 39 >>>>>>> 94 40 >>>>>>> 2111 53 39 34 36 >>>>>>> 43 43 >>>>>>>> pmsVSN=vsn::vsnMatrix(pms) >>>>>>> vsn2: 899636 x 6 matrix (1 stratum). Please use 'meanSdPlot' >>>>>>> to verify the fit. >>>>>>>> class(pmsVSN) >>>>>>> [1] "vsn" >>>>>>> attr(,"package") >>>>>>> [1] "vsn" >>>>>>>> pmsVSN >>>>>>> vsn object for n=899636 features and d=6 samples. >>>>>>> sigsq=0.026 >>>>>>> hx: 899636 x 6 matrix. >>>>>>>> eset=rma(pmsVSN, background=FALSE,normalize=FALSE) >>>>>>> Error in function (classes, fdef, mtable) : >>>>>>> unable to find an inherited method for function ?rma? for >>>>>>> signature ?"vsn"? >>>>>>> >>>>>>>> library(vsn) >>>>>>>> meanSdPlot(pmsVSN) >>>>>>> KernSmooth 2.23 loaded >>>>>>> Copyright M. P. Wand 1997-2009 >>>>>>> >>>>>>>> sessionInfo() >>>>>>> R version 2.15.2 (2012-10-26) >>>>>>> Platform: i386-apple-darwin9.8.0/i386 (32-bit) >>>>>>> >>>>>>> locale: >>>>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/ >>>>>>> en_US.UTF-8 >>>>>>> >>>>>>> attached base packages: >>>>>>> [1] stats graphics grDevices utils datasets >>>>>>> methods base >>>>>>> >>>>>>> other attached packages: >>>>>>> [1] vsn_3.26.0 pd.mogene.1.0.st.v1_3.8.0 >>>>>>> RSQLite_0.11.2 DBI_0.2-5 >>>>>>> [5] oligo_1.22.0 Biobase_2.18.0 >>>>>>> oligoClasses_1.20.0 BiocGenerics_0.4.0 >>>>>>> [9] limma_3.14.3 >>>>>>> >>>>>>> loaded via a namespace (and not attached): >>>>>>> [1] affxparser_1.30.0 affy_1.36.0 >>>>>>> affyio_1.26.0 BiocInstaller_1.8.3 Biostrings_2.26.2 >>>>>>> [6] bit_1.1-9 codetools_0.2-8 >>>>>>> ff_2.2-10 foreach_1.4.0 GenomicRanges_1.10.5 >>>>>>> [11] grid_2.15.2 IRanges_1.16.4 >>>>>>> iterators_1.0.6 KernSmooth_2.23-8 lattice_0.20-10 >>>>>>> [16] parallel_2.15.2 preprocessCore_1.20.0 >>>>>>> splines_2.15.2 stats4_2.15.2 tools_2.15.2 >>>>>>> [21] zlibbioc_1.4.0 >>>>>>> >>>>>>> >>>>>>> [[alternative HTML version deleted]] >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioconductor mailing list >>>>>>> Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> >>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>> -- >>>>>> James W. MacDonald, M.S. >>>>>> Biostatistician >>>>>> University of Washington >>>>>> Environmental and Occupational Health Sciences >>>>>> 4225 Roosevelt Way NE, # 100 >>>>>> Seattle WA 98105-6099 >>>>>> >>>> >>>> -- >>>> James W. MacDonald, M.S. >>>> Biostatistician >>>> University of Washington >>>> Environmental and Occupational Health Sciences >>>> 4225 Roosevelt Way NE, # 100 >>>> Seattle WA 98105-6099 >>>> >>> >> > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 >
ADD REPLYlink written 6.9 years ago by José LÓPEZ110
That command should probably read pm(raw) <- pmsVSN instead (mind the s) but it seems the real issue is there: pm(raw) <- pmsVSN Error in function (classes, fdef, mtable) : unable to find an inherited method for function ?pm<-? for signature ?"GeneFeatureSet", "missing", "missing", "vsn"? Nico --------------------------------------------------------------- Nicolas Delhomme Genome Biology Computational Support European Molecular Biology Laboratory Tel: +49 6221 387 8310 Email: nicolas.delhomme at embl.de Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany --------------------------------------------------------------- On Jan 11, 2013, at 4:31 PM, Jos? L?PEZ wrote: > Dear Jim, > > Thank you for the advise on the background correction step. > I already tryed before the whole Benilton's code but it doesn't work at the following step. > >> pm(raw) <- pmVSN > Error: object 'pmVSN' not found > > May I ask you what this step is doing? Does it replace the pm matrix in the raw ExpressionFeatureSet by the normalized one? > > Thank you in advance for your time and your kind help, > > Jose > >> library(limma) >> library(oligo) >> Data=read.celfiles(list.celfiles()) > Loading required package: pd.mogene.1.0.st.v1 > Loading required package: RSQLite > Loading required package: DBI > Platform design info loaded. > Reading in : ABRNA1.CEL > Reading in : ABRNA2.CEL > Reading in : ABRNA3.CEL > Reading in : ABRNA4.CEL > Reading in : ABRNA5.CEL > Reading in : ABRNA6.CEL >> pms=pm(Data) >> raw=backgroundCorrect(Data,"rma") > Background correcting... OK >> pms=pm(raw) >> pmsVSN=vsn::vsnMatrix(pms) > vsn2: 899636 x 6 matrix (1 stratum). Please use 'meanSdPlot' to verify the fit. >> pm(raw) <- pmVSN > Error: object 'pmVSN' not found >> pm(raw) <- pmsVSN > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function ?pm<-? for signature ?"GeneFeatureSet", "missing", "missing", "vsn"? >> pmsVSN > vsn object for n=899636 features and d=6 samples. > sigsq=0.1 > hx: 899636 x 6 matrix. >> head(pms) > ABRNA1.CEL ABRNA2.CEL ABRNA3.CEL ABRNA4.CEL ABRNA5.CEL ABRNA6.CEL > 2106 7.853059 7.635413 5.221570 5.160448 5.978796 5.767533 > 2107 5.990083 4.764031 4.659925 5.160448 7.067603 5.903628 > 2108 4.867173 4.587342 5.023095 4.762256 5.978796 6.045105 > 2109 10.657556 8.827158 7.679404 6.124607 11.523816 6.045105 > 2110 12.538396 13.906774 6.147958 5.860049 38.764281 6.843026 > 2111 10.241785 6.356910 4.836138 5.160448 7.067603 7.405633 >> class(pms) > [1] "matrix" >> ls() > [1] "Data" "pms" "pmsVSN" "raw" > >> sessionInfo() > R version 2.15.2 (2012-10-26) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] pd.mogene.1.0.st.v1_3.8.0 RSQLite_0.11.2 DBI_0.2-5 oligo_1.22.0 > [5] Biobase_2.18.0 oligoClasses_1.20.0 BiocGenerics_0.4.0 limma_3.14.3 > > loaded via a namespace (and not attached): > [1] affxparser_1.30.0 affy_1.36.0 affyio_1.26.0 BiocInstaller_1.8.3 Biostrings_2.26.2 > [6] bit_1.1-9 codetools_0.2-8 ff_2.2-10 foreach_1.4.0 GenomicRanges_1.10.5 > [11] grid_2.15.2 IRanges_1.16.4 iterators_1.0.6 lattice_0.20-10 parallel_2.15.2 > [16] preprocessCore_1.20.0 splines_2.15.2 stats4_2.15.2 vsn_3.26.0 zlibbioc_1.4.0 > > > ***************************************************** > Jos? P. L?PEZ-ATAYALA > Instituto de Neurociencias > CSIC - UMH > Avda. D. Santiago Ram?n y Cajal, S/N > E-03550, Sant Joan d'Alacant > Alicante, Spain > jose.lopez at umh.es > http://in.umh.es/grupos-detalle.aspx?grupo=30 > (34) 965 919 531 > > El ene 11, 2013, a las 3:59 p.m., James W. MacDonald escribi?: > >> Hi Jose, >> >> Let's say you followed Benilton's code from https://stat.ethz.ch/pipermail/bioconductor/2010-June/033936.html >> >> library(oligo) >> cels = list.celfiles() >> raw = read.celfiles(cels) >> raw = backgroundCorrect(raw, "rma") ## I added this - you might want BG correction >> pms = pm(raw) >> pmsVSN = vsn::vsnMatrix(pms) >> pm(raw) <- pmVSN >> rm(pms, pmsVSN) >> >> you now have an ExpressionFeatureSet with normalized data that you want to summarize. You can then >> >> eset <- summarize(raw, method = "medianpolish") >> >> See >> >> ?summarizationMethods >> >> for more information. >> >> Best, >> >> Jim >> >> >> On 1/11/2013 6:17 AM, Jos? L?PEZ wrote: >>> Dear Benilton, >>> >>> I am using oligo for Mouse Gene 1.0ST arrays. In addition to RMA, I would also like to pre-process with vsn. I have seen previous threads related to this question in the past, (https://stat.ethz.ch/pipermail/bioconductor/2010-January/031100.html, https://stat.ethz.ch/pipermail/bioconductor/2010-June/033936.html), but unfortunately, I am not bioinformatician and, although I read oligo and vsn manuals, it is not easy to me to follow up to summarize the vsn object. >>> May you (or someone else) please, give me some additional clue to sumarize the vsn object using the oligo package. >>> >>> Thank you very much in advance for your time and your kind help, >>> >>> Jose LOPEZ >>> >>> ************************** >>> >>>> list.files() >>> [1] "ABRNA1.CEL" "ABRNA2.CEL" "ABRNA3.CEL" >>> [4] "ABRNA4.CEL" "ABRNA5.CEL" "ABRNA6.CEL" >>> [7] "Limma_FilterBefore_H2BGFP_jla_vsn.R" >>>> library(limma) >>>> library(oligo) >>> Loading required package: BiocGenerics >>> >>> Attaching package: ?BiocGenerics? >>> >>> The following object(s) are masked from ?package:stats?: >>> >>> xtabs >>> >>> The following object(s) are masked from ?package:base?: >>> >>> anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, >>> mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, >>> setdiff, table, tapply, union, unique >>> >>> Loading required package: oligoClasses >>> Loading package bit 1.1-9 >>> package:bit (c) 2008-2012 Jens Oehlschlaegel (GPL-2) >>> creators: bit bitwhich >>> coercion: as.logical as.integer as.bit as.bitwhich which >>> operator: !& | xor != == >>> querying: print length any all min max range sum summary >>> bit access: length<- [ [<- [[ [[<- >>> for more help type ?bit >>> Loading package ff2.2-10 >>> - getOption("fftempdir")=="/var/folders/U+/U+SFMmqcEbKkSysJQ3OYbk+ ++TQ/-Tmp-//RtmpKgQzWD" >>> >>> - getOption("ffextension")=="ff" >>> >>> - getOption("ffdrop")==TRUE >>> >>> - getOption("fffinonexit")==TRUE >>> >>> - getOption("ffpagesize")==65536 >>> >>> - getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes >>> >>> - getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system >>> >>> - getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system >>> >>> Welcome to oligoClasses version 1.20.0 >>> Loading required package: Biobase >>> Welcome to Bioconductor >>> >>> Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see >>> 'citation("Biobase")', and for packages 'citation("pkgname")'. >>> >>> ================================================================== ====================================================== >>> Welcome to oligo version 1.22.0 >>> ================================================================== ====================================================== >>> >>> Attaching package: ?oligo? >>> >>> The following object(s) are masked from ?package:limma?: >>> >>> backgroundCorrect >>> >>>> Data=read.celfiles(list.celfiles()) >>> Loading required package: pd.mogene.1.0.st.v1 >>> Loading required package: RSQLite >>> Loading required package: DBI >>> Platform design info loaded. >>> Reading in : ABRNA1.CEL >>> Reading in : ABRNA2.CEL >>> Reading in : ABRNA3.CEL >>> Reading in : ABRNA4.CEL >>> Reading in : ABRNA5.CEL >>> Reading in : ABRNA6.CEL >>>> pms=pm(Data) >>>> class(pms) >>> [1] "matrix" >>>> head(pms) >>> ABRNA1.CEL ABRNA2.CEL ABRNA3.CEL ABRNA4.CEL ABRNA5.CEL ABRNA6.CEL >>> 2106 46 43 36 36 37 33 >>> 2107 38 32 33 36 43 34 >>> 2108 31 31 35 34 37 35 >>> 2109 54 46 45 40 58 35 >>> 2110 58 55 40 39 94 40 >>> 2111 53 39 34 36 43 43 >>>> pmsVSN=vsn::vsnMatrix(pms) >>> vsn2: 899636 x 6 matrix (1 stratum). Please use 'meanSdPlot' to verify the fit. >>>> class(pmsVSN) >>> [1] "vsn" >>> attr(,"package") >>> [1] "vsn" >>>> pmsVSN >>> vsn object for n=899636 features and d=6 samples. >>> sigsq=0.026 >>> hx: 899636 x 6 matrix. >>>> eset=rma(pmsVSN, background=FALSE,normalize=FALSE) >>> Error in function (classes, fdef, mtable) : >>> unable to find an inherited method for function ?rma? for signature ?"vsn"? >>> >>>> library(vsn) >>>> meanSdPlot(pmsVSN) >>> KernSmooth 2.23 loaded >>> Copyright M. P. Wand 1997-2009 >>> >>>> sessionInfo() >>> R version 2.15.2 (2012-10-26) >>> Platform: i386-apple-darwin9.8.0/i386 (32-bit) >>> >>> locale: >>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] vsn_3.26.0 pd.mogene.1.0.st.v1_3.8.0 RSQLite_0.11.2 DBI_0.2-5 >>> [5] oligo_1.22.0 Biobase_2.18.0 oligoClasses_1.20.0 BiocGenerics_0.4.0 >>> [9] limma_3.14.3 >>> >>> loaded via a namespace (and not attached): >>> [1] affxparser_1.30.0 affy_1.36.0 affyio_1.26.0 BiocInstaller_1.8.3 Biostrings_2.26.2 >>> [6] bit_1.1-9 codetools_0.2-8 ff_2.2-10 foreach_1.4.0 GenomicRanges_1.10.5 >>> [11] grid_2.15.2 IRanges_1.16.4 iterators_1.0.6 KernSmooth_2.23-8 lattice_0.20-10 >>> [16] parallel_2.15.2 preprocessCore_1.20.0 splines_2.15.2 stats4_2.15.2 tools_2.15.2 >>> [21] zlibbioc_1.4.0 >>> >>> >>> [[alternative HTML version deleted]] >>> >>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> University of Washington >> Environmental and Occupational Health Sciences >> 4225 Roosevelt Way NE, # 100 >> Seattle WA 98105-6099 >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 6.9 years ago by delhomme@embl.de1.2k
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